If I run my RCA from head unit to my subwoofer amp and use its built in low pass filter, then will it output the original signal or will output just the low freq's through the RCA out that would go to my next amp.

Should pass everything. What's the make and model?

Its a Directed Audio 350d.

Should pass everything. The only amp I've seen that didn't was some total POS flee market junk.

It should pass everything, I had mine set-up that way w/ my old HU (because it only had one pre-amp) and it worked fine.

Im yet to see an amp without a straight through output on it. On my setup i have 3 amps daisy chained and all different brands too

(yes i do have a ghetto setup but it works for me)