So right now I have tickets with park passes booked for June. IF I decide to book on property later and add it to my MDE, will that mess up my park passes? Right now I have them as an offsite guest. Slightly concerned that becoming an on-site guest might screw up the system.
No that should be fine. As long as you have valid admission linked for the days you have reservations, they will stay in place. I think the way the system works is that when you add your on site reservation, your reservations become “on site” and so in theory if you had an AP or something, you could book additional days using your three AP reservation bucket.
ETA: I never added an on-site stay, but I did switch on-site stays (added a reservation and then cancelled the original one) multiple times and it never affected my park reservations.
I have even cancelled a ticket/resort package and park reservations made on those tickets were not affected.