1. You have to be sure that the speaker level signal that you're feeding the amp contains sub bass; that it's not crossed over somewhere along the way.
2. High level inputs on amplifiers are provided as a courtesy and are notoriously faulty in providing a good conversion in every vehicle. Aftermarket LOC's are the route one should take if the OEM deck is to remain in the mix.
3. The amp's high level input is a converter. It uses the speaker level signal in the OEM speaker wires and converts that signal to low level so that the amp can use it. It either works right or doesn't. Since it's a freebie addition on an amp, it is barebones as far as features go. Don't spend much time on troubleshooting this device...the only thing you have to make sure of is that you're not feeding it a higher range of freqs than the sub is capable of playing.
4. Always read the manual instructions.
5. Usually it is a case where the stock system is not compatible with adding an aftermarket amplifier, like a Bose system. Or when there are separate OEM amplifiers in the path and you are using the wrong signal, like the signal to rear speakers when you should be using the signal to the OEM sub.
6. This is most important: If a new deck is planned, wait until you get it and install it. Haste makes waste. This sounds like a situation where your friend is too anxious to start hearing the results and hasn't put all the pieces of the puzzle together yet. If the new deck is not far off in the future, wait for it and put this system together once and for all. There is a great deal of work that goes into setting up a sub bass addition when using a factory deck, starting with buying an aftermarket LOC that is compatible with the car's OEM system.
7. If you decide to invest in going this route (using the stock deck), start by getting the right LOC. You'll find one in the David Navone line-up, for one. And you'll find that when you set the amp gains to match the OEM deck that the procedure will be a bit different than using an aftermarket deck: the highest clean signal level will be at about the halfway point on the OEM deck, and you will set the amp gain to match it at that point.
Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.