is it the pedal or the pick ups or both?

[bassguitarded]

i just changed my bass preamp to a Aggie OBP-3 with an active passive switch.... my Bass big muff has been a little noisy, but now when my bass is in passive mode the squeal is so high pitch and loud that it cuts into my long notes and i cant play any rests at all! when active the noise lessens to a low hum but is still pretty noticeable.
i am ordering new pickups this weekend (5 string BL jazz 1/4lbs) so I'm hoping some of this is solved by the new set. but if it isn't, then what can i do to stop the squelching.... noise suppressor? gate? which one? before or after the pedal? would the noise suppressor cut some of my fuzziness or sustain? i hope not!
i want to write some droney stuff with some ultra silent rests so when the bass comes back it feels like a punch in the gut. but right now all i get is "sqeeeeeeeeeeeeeee" when i'm not playing. help!