This can sometimes happen, it is just a minor glitch in communication between the plugin and the game. Simply exit the game, log back in, and try again.
No. The MakePlace plugin cannot interact with your inventory or your house storage so make sure all items are placed down somewhere, and dye them first.
It doesn't matter, MakePlace will read which items are dyed which colour and place them appropriately.
Not all of the available layouts will work in-game. To avoid these issues, we suggest loading any downloaded json files into the standalone app first to check item placement and if the file is still readable.
Keep in mind also that some designers do not take into account the in-game restrictions. This will cause your layout to look like it's fallen apart in-game when there is glitching that does not meet the in-game restrictions.