Disclaimer: This is based on my personal experience of what my Company mates and I have come across while trying to protect our land from invaders. Some information may not be 100% correct but so far I have not seen evidence to dispute the workings of this system. Also note that this information is current as of v9.3 with future v10.0 in mind.
For the purpose of this tutorial, I will be referencing the venn-diagram image below and the information it holds. From here on out I will use the following references:
Green circle as "A"
Red circle as "B"
Yellow circle as "C"
Blue circle as "D"
Example: If I say "AB" I am referencing the area covered by both "A" and "B".
As a pirate surviving the rough landscapes and the perilous seas you have numerous options afforded to you in regards to choosing a home location. You may do the following:
Remain at Starter Freeports (Forever stuck at max level of 8)
Live the Sea Life on boats
Live on Lawless territory
Claim area outside of the above mentioned areas (can claim open sea)
At Starter Freeports, you cannot claim any land nor does it allow building of any sort as it is not claimable or lawless.
Living at sea is possible. You can trade materials in to obtain yourself a raft (even a Ramshackle Sloop! coming soon) at a Starter Freeport by speaking with the Shipyardsman at the end of the dock. With this, you are able to place a bed, a campfire, some storage, a water barrel - and a few other things if you can fit it. Now that you have a built up mobile home you can live out on the open water. Keep in mind that all ships gradually take durability damage over time and that damage is increased based on whether or not you are anchored, in a claimed area and/or out in the water. The ideal method for this would be to find a piece of land to anchor to when you log off for the night.
Living in lawless territory is not for the faint of heart. This method does not allow for claiming land with Claim Flags; instead you use the size of your base to claim an area. Say you choose an area within a lawless territory and you place some foundations and build yourself a little hut to call home. This building will decay over time if you do not visit it / come online. However, other players will not be able to build right next to you. You are provided with a small area of effect (AoE) around your foundations that prevents enemies from building right next to you. The tricky and possibly very costly part about living in lawless is that resources around you are NOT affected by your base or you! Resources (including animals, passives and aggressives) will still respawn causing trees and brushes to protrude through your floors. This is also very beneficial as you can be creative with your terrain and build around the foliage for pretty awesome layouts.
Now onto the meat of this tutorial and the original reason for this post - PvE Claim Flags.
In areas you are able to claim land, you are unable to build without claimed land. If you find yourself needing to shack up due to harsh travels and you come across an island packed full of claim flags, you will find yourself having to steal claims in order to obtain a bit of land to build on. Or maybe you've found yourself a nice location and its free to claim. There are a few mechanics you need to know in order to do this.
You can see claimed land by bring up your map with "M" and looking for red circles. You can see these same circles in person by holding "H" and looking out into the world. You will see a few different colors throughout your time. I will explain these shortly. Finally, by pressing "F1" you will bring up a claim flag that you can place down.
If the land is free, you can simply place the flag and wait 10 minutes to claim your first bit of land! You do not need to be within the circle in order to claim. However, if any other player outside of your company or alliance walks into your circle, the claim will be contested. If you are not within that claim, your claim will begin to fail and you may lose out on that bit of land. if there is enemy territory nearby, you will either have to place your claim flag within that enemies territory, or travel far enough away in order to place your own such that it will contest the enemy territory. This is where different colors come into play, which you can see by holding "H". Note that these colors do not correspond to the venn-diagram image.
Green circles are areas you have claimed. Blue circles are areas you are attempting to claim. Yellow circles are areas other players are trying to claim within your claimed areas. Red circles are all other claimed areas other than your own company's - yes this includes alliance members (This should be fixed as allies can steal land).
Alright - so you have finally claimed a bit of land. At this point your claim is safe from other pirates wanting to steal your land for 3 real world days - 72 hours! From the moment you claim is successful, that claim will begin accruing time. Starting at 0, time will tick negative until it reaches -259,200 seconds (72 hours). During this time, you do not to be within the circle in order to maintain that claimed area. After 3 days, that claim can be contested by other players and you will likely be forced to protect your land. How do you do such a thing on a PvE server?! No worries - there are ways. As long as a member of your company remains within this new claim of yours, no one can ever steal it from you. Regardless of whether or not you are online or offline - your character remains where you logged. This means you can put together what I like to call a "Claim Building" - or also referred to as a logoff room.
Lets say you have claimed areas "AB" but you're solo! Ah crap! You have TWO areas yet you are but one person! No worries! Follow the venn diagram. Do you see how "AB" are overlapping? Build your Claim Building within the overlapping sections of "AB" and use that as your main place to logoff. At this point no enemy will ever be able to steal "A" or "B" from you. This is where you can get even more land for yourself even as a solo player. You find yourself needing more land, or even water to build shipyards in, so you expand your claim to "ABCD" and you find that your previously built Claim Building falls outside of the new area. You can build yourself a new Claim Building in the center of ALL 4 of the circles! See how they overlap? Alternatively, you can find yourself a company mate to join you and build them their very own Claim Building. You could place this new building where "CD" overlap and thus be covering all 4 with 2 separate logoff rooms.
Do not let this fool you though. Once you come online and begin moving about - your land is in danger of being contested. If someone attempts to steal your land while you're not there you will have to find your way back to contest it! There will be a notification that someone is attempting to steal your territory, so as long as you're paying attention, you should have plenty of time to react. You will have 30 minutes to get back to your claim in order to contest it. Once this 30 minutes is up, you lose your land and their claim timer (10 minutes) begins. Say this enemy of yours has placed a flag on the NW side of "A" but their claim also covers the building you have between "AB". If the enemy successfully claims "A" you will lose that circle and potentially the building. If they are successful, their newly claimed area has the 3 day protection as yours did when you first started.
I will try my best to correct any inaccuracies within this post and update it as time goes on. If you have questions, suggestions or concerns, please let me know!
I hope this helps alleviate some of the confusion surrounding the PvE Claim Flag system and helps you maintain your claims - or steal claims - whatever floats your boat!