If you record both, then you really have to punch-in both, in most home recording setups. There's usually just too much bleed, even if you've got a plugged in acoustic, the vocal track is going to have acoustic guitar, and if it suddenly disappears in the overdub, it will be noticeable, except if there's a much bigger mix yet to come. (You *might* be able to compensate by raising a plugged-in guitar track slightly, but it'll be less work to just do both, at least that's my experience.)
Just set up everything like the original recording, if you're doing this in a different session, so the levels are about the same. I create new tracks for both instruments, and automate the original vocal level down a lot where the overdub will be. Practice playing and singing along to the original and making the correction a time or two, than do a take to get it right. Edit the new take down to the overdub, and, depending on your DAW, splice both the guitar and vocal in using clip gain to match the original and crossfades. In Logic, I can "pack" the new tracks into the original as a "take folder" so creating a comp is just a couple mouse swipes - probably something similar in some others, but the manual method works too.