Since this mod lets you build shacks anywhere you want, it's almost compatible with all mods. There are some slight issues that may arise using certain mods that I will address here:

Jaxonz Positioner (and other object movers)

Issue: These mods were compatible (and encouraged to use) in version 1, however in version 2 all items include AI navigation information attached to them that these mods will not move, therefore rendering them completely incompatible with shack items. Note that you can still use this for everything in Skyrim, except the furniture built with this mod.
Workaround:
From version 2 onwards, you can move all items using built in tools such as “Move Shack Items” and “CShacks Master Spell” spells.

Follower mods

Issue: This mod is scripted so your vanilla followers will follow you into the shacks. If you're using certain custom followers or follower overhaul mods, they might not.
Workaround:
Enter your follower's command mode (by default you have to hold “E” while aiming at them), and instruct them to activate the shack door.

Economy mods

Issue: The shacks and other furniture are tweaked for vanilla Skyrim purchase prices. There are some vanilla perks and economics mods which make trading either easier or harder. Using the vanilla ones or mods that make mild adjustments is ok, but using a mod to make trading extraordinary difficult might make the shacks ridiculously expensive to the point of being more expensive than full blown player homes or downright impossible to acquire.
Workaround: Use console commands to acquire (or purchase) the goods. View the console commands section for more info.

Location mods

Issue: There might be some compatibility issues with mods that alter the same cells that are used by carpenters. I have double checked to make sure the following mods remain compatible: Skyrim Flora Overhaul, Lanterns of Skyrim, Expanded Towns and Cities. I have also tried to use cells that don't seem to be important for editing by other mods to avoid incompatibilities as much as possible.
Workarounds: If you are using a mod that does edit the same cell as the carpenters, you can use one of the “compatibility version” of this mod when installing. The “interior only” version removes all carpenters from exteriors and puts them in interiors, making sure it stays compatible with all mods that alter skyrim's exteriors. Specifically, this version is compatible with Alternate Start's “Camping in the Woods” scenario.
Whiterun only version removes all carpenters besides the one in Warmaiden's, Whiterun. If you have a mod that alters Warmaiden's and it isn't compatible, use console commands to acquire the starter kit. View the console commands section for more info.

Alternate start mods

Issue: There isn't any real issue. Just that since you don't start in Helgen, you won't see the carpenter at the start of the game
Workaround: If you want the starter shack with your alternate start mod, use the master spell to acquire the starter kit. This kit places a carpenter at your current location, and he sells a starter shack for a low price. View the console commands section for more info.

Frostfall

Issue: The campfire burns forever and is therefore a better campfire than those of frostfall's.
Workaround: There isn't any real workaround as I don't consider this an issue. There are other campfires in Skyrim that burn forever, such as those of the bandits. It always bugged me that the bandits would get to have eternal campfires while the player had to keep adding firewoods to theirs.

However, pay attention that the campfire in this mod is inherently different than the one from frostfall, in that the one from frostfall is suited for traveling, while this mod's is suited for a warm player home. The campfire offered by this mod is quite expensive, heavy, and can only be acquired at certain locations. It doesn't make much sense to travel with one of these instead of some firewoods, and the chances of you wanting to return to a campfire is not much unless you want to make that place your home.

On the other hand, this campfire fixes the issue that in frostfall, your player homes would be considered “safe”, but you wouldn't be able to turn a place in the wilds into a safe place. As the aim of this mod is just that, I felt that adding this campfire was rather necessary.