New to this. How do I stack my stuff?

You could cut the speaker cables (shorter is better) and clamp the bare wire in the speaker terminals. Otherwise, not a big deal. Stacking components is not the best. I would move the preamp to the transformer-free side of the CD player. Replace the power cords with OFC cords like BLE Design on eBay for $30 each.

@n80- I guess you can ’stack’ equipment, but I always thought that was bad practice for a variety of reasons- heat, interference among components, etc. And your amp, though on wooden strips, is still cushioned by the carpeting- better, I think to spike through the carpet to the underlying floor boards using some kind of spike and constrained layer platform. (All that means is that the materials of the platform have different resonance characteristics, with some sort of elastic compound in the middle, so you are not hearing the sound of one particular material). You can actually make some of this stuff yourself if you are resourceful.
Some people like the sound of certain kinds of wood. You can read about people’s impressions of the sound of various materials simply by searching --maple or butcher block or acrylic, etc.
You don’t necessarily need specialty equipment stands. But the furniture you use to support the equipment will impart a character to the sound-- there was a school of thought with the old Linn turntable about using a very light, flimsy table beneath it. Others like massive pieces-- I used to use a huge old mahogany prayer table to support a 250 lb turntable. It required some sorbothane under the feet of the table itself, not under the gear. The gear sat on top of the prayer table without additional isolation or other material (except for the turntable, which was a special case).
Putting sorbothane under a piece of gear will change the sound. It may be better or not. Certainly cheap enough to experiment with, and you don’t necessarily have to buy the audiophlle branded products to do this. Read up a bit on the difference between coupling and decoupling--I experimented 5 or so years ago, maybe longer, with a bunch of different ’footers’ beneath the power supply to my phono preamp. From an old audiophile expensive cone -the Goldmund, to Herbies footers, to Aurios (don’t remember the model it was like an enclosed roller block so the equipment would shimmy sideways), to some HRS stuff, to Vibrapods (puck and cone) to Stillpoints SS. Believe it or not, the Vibrapod with cone was pretty decent in that particular set up and dirt cheap; the Aurios lent unbelievable clarity but created a strident edge to the sound; the Herbies sounded ’mushy’ to me; the Goldmunds didn’t seem to do much at all. I found the Stillpoints to give me the clarity without the drawbacks of the Aurios. They are money, though.
Hope that helps.
PS: probably not a bad idea to get Jim Smith's book, Get Better Sound. You can order it from Amazon. Even if some of it is known to you, I'll bet you'll learn a few things. Jim's thing is all about 'set-up' and 'playing the room.' That goes beyond your questions-- namely how to 'voice' the system and take advantage of the room, acoustically. But, Jim gets down into all the details of system set up in the process. Well worth reading. 

I agree that using Sorbothane under a component will affect the sound. IME, music will sound less lively, less open.
Herbies Extra firm Tenderfeet would provide good Isolation in your
situation.
http://herbiesaudiolab.net/compfeet.htm

Try to replace the side table so that each component has it's own shelf.

When I had my belt drive CEC cd player in the system Vibrapods without cones worked okay but Boston Audio graphite tune blocks were better in every respect. I use a combination of a 3" thick maple block and Boston Audio tune blocks under my Nottingham turntable and have no intention of changing this set-up. You can also try good brass cones under you player but it may ring, Audiopoints maybe. I use them under my integrated amplifier. If you can't avoid stacking you might want to put something under the feet of your pre-amp, maybe some cork/hard resin blocks like Mapleshade sells, and I got something very similar on Audiogon for my PS Audio power plant regenerator. As for the amp, I don't know if it is realistic to put it on a good spiked amp stand.

The sound must be very alive even if it is not exactly pure. To have both you would need a complicated and expensive set-up. Some swear by active K Minus and Herzan platforms. I think Whart has the former under his turntable.