Yes, there is a way to do that.
Call Disney Reservations and ask them to make a "traveling with" notation on each reservation, referencing the other reservation number.
Make sure you let them know the EXACT nature of the request. For example, if you say you want to be "near" each other, you could wind up in the same building, but not all that close.
If you want to have rooms next to each other that have a door between then, tell reservations that you want "connecting" rooms. If you say you want rooms "next to each other" or "adjacent " that could mean rooms next door to each other but without a door between them. Words matter.
Once you've had the request(s) added to both reservations, DO NOT make any requests when you do on-line check-in; as doing so will override the requests made through Disney Reservations.
When you arrive, and before anyone enters either room, go to the front desk and verify that the location of the rooms is acceptable. If not, ask if it's possible to have your request met. They may be able to change your rooms.
While these are just requests, Disney tries to accommodate as much as they can. I once had 5 separate room reservations at the same resort for wedding guests arriving over the course of 3 days. I asked to have the rooms be as close as possible to each other. All 5 were in a row.
Steve