If you are asking if you have to use the padded input (depending on the amp, -15 DB for example) on the amp with pedals, the answer is no as Mr. Foxen said.
Sometimes you have to be careful. If the level is too hot from the bass you can distort the input of the pedal. If the signal is too hot out of the pedal, it can overwhelm the input of the amp.
Use your ears and adjust the volume/gain levels to give you the best sound. Use whatever input on the amp that works the best.
Official Ampeg Portaflex Club #89