New to this. How do I stack my stuff?

I'm new to hifi. I've asked a lot of questions here and some of you may already know my situation but I got the following by chance and for free: Audio Research LS16 tube pre-amp, Arcam CD92 cd player, Madrigal Proceed HPA2 amp. 

It is all up and running and I'm loving it. Now just trying to maximize the little things that I can. For instance, speakers had spike stands but spikes were missing so I made a set.

Now I read in the CD manual that it recommends sorbothane feet and says sound quality will be better.

I'm now figuring out that placement of components is important and that proper stands, expensive ones, are best. Well, expensive stands are not going to happen. But I can try to make accommodations that are cheap and won't turn the room upside down.

Here is how it is all situated now...let the ridicule flow, but keep in mind that I am space limited to a serious extent. Was not sure I'd get the system in my house at all:

The (very) heavy Proceed amp is sitting on a carpeted floor on strips of wood which raise the bottom of it well above the carpet. It is higher above the carpet than it would be above a hard surface just on its own feet.

The CD player is sitting on a small, simple, wooden, antique side table. It is sturdy. The pre-amp is on top of the CD player. I have no idea what this might mean in terms of SQ but the CD player actually puts out a fair amount to heat which rises up into the pre-amp of course. That concerns me.

So other than getting some sorbothane feet for the CD player, what else would be a priority here?

Finally are there issues with which cables contact which cables, how much speaker cables are looped, etc. (Most of the cabling is Transparent Super Bi-wire.)

Thanks for any assistance.