Being a new twin in a non-competitive market, I may not be most qualified to answer but....
It certainly would be cause for concern if your booker now books your largest competitor and you are the smaller account by so large a margin. A conflict of interest seems inevitable. Booking being what it is today, your booker need not be located in your area, but he/she should have good relationships with the regional film reps from your area.
Booking appears to us to be so crucial, especially in small theaters, because in addition to the percentage and rental fees, small houses need to turn films more often to keep the locals coming in often. We concern ourselves less up front with the percentage we pay (nearly always standard across the nation/region) and more with getting as short a first-run as we can. We know we can always increase the run if it goes well but can rarely get out of a four-weeker after two or three weeks if it doesn't perform. This is what we have our booker focus on.
Having recently switched to first-run, your booker also has to take alot of effort to educate the studios as to your new profile, including house allowances, etc.
As booking is one of the things we can't directly control (I'm not nearly experienced enough to book for myself yet), the right booker is crucial to our existance!