You can also ask MS to annotate both reservations with "travel with" ... (they may have done so already if you booked both ressies at the same time)...
I annually take my DD and 2 DGKs to Disney, and I never request that we be near each other (we've stayed at OKW, BLT, SSR and BWV)...and they always put us next to each other and note that they've "granted my request" (which I've never made)...
To us, having our villas close to each other is not a big deal (don't mind at all when we are next to each other, but in no way "need" it)...I MUCH prefer ground floor over higher floors, so I usually request that...probably 4-5 (out of 8-9) trips, they've told me that putting us next to each other, "as you requested" (only I didn't) prevented them from giving me a ground floor.
We've always sorted it out and it's never been a "problem"--but I have noticed that making the two reservations at the same time results in an "automatic" Disney-generated request that we be put next to each other...and they've told me (at check-in) that it's because there was a "travel with" note on my reservation...
Good luck!