> "Does this work with existing characters?"
Yes, but you have to take a few measures:
- For Walls mods, there is no way to learn the Hull Station blueprints so far, so you have to spawn one by using the console command "/spawnitem imm_{species}hullST", where {species} is your species name (some modded species names are abbreviated. Refer to this document[pastebin.com] to make sure)
- For Ships mods, you have to either upgrade or reset your ship for all changes to take effect (upgrading being the more practical one). To reset your ship:
* Make sure you retrieved and stored anything you don't want to lose outside of the ship, and that the character whose ship you want to reset was the last one you played;
* Go to your "Starbound/storage/player" folder (on Steam, that'd be "Program Files\Steam\steamapps\common\Starbound\storage\player") - you should see a bunch of gibberish .player and .shipworld files;
* Sort the files by date, and delete the most recent .shipworld file, along with all .bak files associated with it.

> Something about installing/uninstalling/updating one of the mods created invisible blocks in some places.
Resetting the ship should fix it, but if the only issue is some invisible blocks, a more practical solution might be to use this mod.

> Ship graphics looks offset from where they should be
Usually caused by another mod overwriting the ship graphics files in a "Ships" mod. Try unsubscribing from any other mod that might be changing those files and see if the issue is fixed. In any case, be sure to report the issue in the Issues thread so that I may update the mod to allow compatibility if possible.

> Ship doors not animating correctly / look weird
Usually caused by another mod overwriting the ship door graphics files in a "Ships" mod. Try unsubscribing from any other mod that might be changing those files and see if the issue is fixed. In any case, be sure to report the issue in the Issues thread so that I may update the mod to allow compatibility if possible.

> Other issues
Make sure you have all required mods for each part of Better Ships. If there's no dependency issues, comment on this, preferably making note of what species you encounter this issue in, what ship stage, and what mods you have that could be conflicting with it.