I wouldn't try to blend active and passive pickups. EMG has both active and passive versions for both P-bass and Music Man style pickups. So whatever you decide to do, both pickups should be the same type: passive or active.
Apparently this bass has a stock onboard EQ preamp, if you want to retain the stock preamp, then order passive pickups. Active EMGs typically don't use an outboard EQ, just a passive tone control. If you want both active pickups and an active EQ, I believe you'll need to use one of EMGs preamps that's made for use with their active pickups.