Non-audiophile needs help with older system.

I recently inherited a number of 10-15 year old high end audio components. I am not an audiophile but do appreciate high end sound. I do not have a dedicated room for this system. But, it was free and I'd like to figure out how to use it without spending a lot of money on it. I am not looking for audio perfection, just to optimize what I have. This will be used for two-channel music only. I'll try to describe the setup as best I can but I'm sure I do not know the proper terminology.

The components are as follows:

Pair of Aerial Acoustics floor speakers. Towers. No model number. I'm thinking 7B maybe. Have contacted Aerial to see if they can help me identify them. They have a tweeter, midrange and two woofers. Rear bass port. Separate connectors for woofers and midrange/tweeter. 

Madrigal Proceed HPA 2 amp. 250 watts. Weighs a ton.There are very large shielded(?) 'biamped'(?) cables from the amp to the speakers.

Audio Research LS16 Stereo PreAmp. There are large shielded XLR cables from the pre amp to the amp.

Onkyo home theater 'receiver' that I do not like. Remote is lost. Set up is tedious.

There is a very basic Arcam CD player and a Sony phono.

I've got it all hooked up. Bass seemed poor just running CD through pre-amp. If I run CD player to Onkyo to pre amp and adjust bass with Onkyo the sound is incredible (to me).

This system will be used for casual listening, CDs, records, radio, and iTunes via cell phone. I know that is like using a Porsche 911 to get groceries....but it was free. And there will be times when I can sit down for serious listening but that will be infrequent.

I plan on replacing the Onkyo home theater receiver with a basic FM Tuner/Bluetooth/receiver (probably a Sony). This will be for radio and iTunes so even though it is probably not a quality unit I don't think that will matter since the input (iTunes) won't be all that great anyway.

My main questions have to do with how to route the CD, the tuner and the phone through the system.

The preamp has RCA input connectors for all three. But if I run the CD and the phono directly through the preamp there is no way to adjust bass and treble and as mentioned running the CD directly through the preamp resulted in great high and midrange quality but low bass. So should I run the CD and phono into the receiver I'm going to buy and then just run the receiver out to the preamp in?

Sorry for the long post and appreciate any help you guys can give.

George