I am installing a mini itx computer in my car and went to wire up the
audio the other day.

I ran the minjack to rca line into the back of my Alpine 9845. There
are only two sets of RCA plugs behind the HU. One labeled for front
speakers and the other labeled for rear/subs. Since I am running subs
already, I just plugged the RCA cable into the remaining plugs.

I turned the Aux option on in my HU and starting playing some music. I
could just barely hear some audio. I messed with all volume settings on
both my HU and computer. It is as if the internal HU amp is not working
for Aux.

In the past, I have experienced this issue with trying to hook wires to
the output rca's of a vcr, not the input. Are the rca's behind the head
unit just for output. With no other visible connection on the HU, where
else would I plug my computer audio into. I did try the rear/sub jacks
as well but to no avail.

I am not in a position to buy another amp either. Does anyone have any
idea as to what the problem is?

Yes, those jacks behind the head-unit are JUST for outputs.

For ALL Alpine decks to run RCA inputs you will need to purchase a special
Alpine adaptor, KCA-121B, and connect it to the Ai-Net connection of your
Alpine. Don't worry, it will only set you back about $15. Then just plug
your device into the RCA inputs on the adaptor and the "AUX" mode will work
fine.

MOSFET

Thanks for the heads up. As it turns out, this Alpine HU is one of the
CDE (E stands for economy I'm assuming) models which means it does not
have Ai-Net or an M-plug. I didn't understand how this model could be
marketed with an Auxillary in option without having inputs in the back.
Then, I noticed something. At a first glance, it looked like a screw
hole, but actually, it was a mini jack plug. Score! Now, I don't even
need any adapters to plug my computer into the HU. I hope this helps
someone else as I feel a tad sheepish.