i would try this first, if this being the case you will need to run a wire from the acc(red) power wire to the boot into the remote terminal. this will allow your amp to be switched on at the same time as the head unit.
if you get this far and still have troubles with the sub working make sure all the correct wires are plugged into the correct terminals.
EG: RCA line sub/w output to RCA channel 1, channel 1 output to sub.
and if you are running your rear speakers off the amp as well have the channels for them to.
is one of the channels able to be bridged?(2 into 1?) thus making it a 3 channel amp.
bridge channels1/2 together (+ve from channel 1 and -ve of channel 2) and use them as your output for the sub. the use the last 2 channels to run your speakers.
any of this help?