If you have the subs/amp tied into a factory head unit, then you need to install a speaker input-to-remote signal output convertor (remote turn on by DEI part# 55000). This piece allows the amp to only come on once a signal is sent to the speakers from the factory HU. Usually when an amp causes sub pop, it is because the amp is getting a turn on signal before it is receiving any music input so it "searches" for a signal.

If you have an aftermarket head unit, you need to recheck all connections (amp ground, etc). If all else fails, you could install a PAC TR-7 universal timer programmable relay box. It will take the remote wire input from the HU and build in a small delay before it sends the signal to the amp. We need more info...