A lot of VA's just use a single aircraft registration for each type (B737, B747, etc..) So you'll be perfectly fine by doing that. phpVMS does support this.
Also when you purchase a VA Schedule, that's going to be the case anyways. Besides, I don't think a lot of pilots really care about the registration of the aircraft they're flying. It doesn't bring any added realism except maybe some role-play value.
Edit: Jim and I replied to your post seconds apart. Read what he wrote - He brings up some good points worth noting.