I’ve edited this topic to more reflect my experience and note that there are ways around my problem. Unfortunately, I went the way of retopology (re-creating the whole mesh by using the existing one to simplify it without losing detail).
TL;DR version: combining meshes is not recommended if you can help it, unless you know what you’re doing (I didn’t). It’s a hassle. Ideally, make your whole sculpture one piece if you can. It will save you a lot of mental aches. BUT if you did make these mistakes, read below to find out how to fix them thanks to @Mark_Jackson and his tutorials.
Long version: I found that using extra meshes after the body is done creates problems down the line with hair. Especially, especially, if your body or any piece is inside of another piece. The problem happens when you come hairs. Because hairs stick through the skin due to underlying faces, they will refuse to be combed. Think grass in concrete: you may move it left or right, but you can’t change its root growth-direction. Booleaning not working to the way I expected (I may just be bad at it), I went through retopology method instead. It’s very time consuming (it took me about 10 hours). And then I found out another issue: my rabbit turned out to have non-symmetrical ears (copy and pasted them, hah) and the tail wasn’t straight (apparently the best way to do this is to rig bones to the tail but keep the tail symmetrical to the X axis). This all happened because I decided to flesh out my rabbit after building the body.
See what happens when you add stuff that is not based off one mesh of metaballs but multiple:
And here’s retopology… I think I’ve spent about 6 hours doing this already and many more hours to go since this is my first time doing it:
So, take-away message: don’t use multiple metaballs or other meshes to add features after the rabbit is done or you’ll have a “hairy disaster” in the later courses.