Could you give a few more details about what's going wrong?
There's a couple issues you may be running into. One may be the navmesh bug, which makes NPC's in custom houses stand around doing nothing if you've entered that space several times in a single play session (basically the navmesh load the first time you enter that session, but will not reload when you return).
Another issue is that your sandbox package might be conflicting with other sandbox packages already running on the NPC. To get a spouse to move, you need to clear the current house sandbox and apply the new one (the vanilla marriage quest does it through a quest alias). Take a look at the script RelationshipMarriageSpouseFIN (or something very close to that) for a sense of how the vanilla spouse moves worked. You might take a look at our http://www.gamesas.com/topic/1351014-adding-spouse-to-new-player-home/ for some ideas about this, too.
Now a problem some of us have run into is that if you assign a custom sandbox to a spouse, another mod will not be able to clear that sandbox because it has no way of knowing its name (so you can switch between your mod and the vanilla houses, but not between two mods, which is fine if you only use one custom house, but a lot of Skyrim players try out multiple houses at once.).
Emma and Amgepo put out their Spouses Can Live Everywhere mod yesterday, which is a nice, elegant solution to the issue. There, too, if you're using that mod, you wouldn't necessarily be able to clear their ai package to replace with a different custom one, but you don't need to because their package will update the location where the sandbox package will be active with a simple spell.
Their package should allow your spouse to interact with all idle markers, crafting stations, and basic furniture.