There are a couple of good threads talking about the Griffen Powermate and the Space Navigator (my personal preference). Check out the Input Devices sub-forum.
As for your questions about how to connect the CarPC audio to your car, how easy in a basic installation, cord management, connecting to the screen....these are all specific to your car and what type of setup you choose.
For some cars, you can get a bezel that replaces your existing stereo and a touchscreen will pop right in. For other cars this isn't an option so folks have had to fabricate a custom bezel/mount from scratch...and this is a lot of work to get it to look good.
I took the REALLY lazy route and utilized my car's existing Navigation System screen as my CarPC's display.
As I'm sure everyone here will agree with, my first suggestion to you is...read. Use the search tool to find threads about the questions you have and the devices you want to install. There are very few "common" problems that haven't been discussed many many times on these forums.
Another suggestion I would make; take a look at the mp3car Gatherings sub-forum. See if there's something going on in your local area. You can learn quite a bit from the forums but, I don't think anything beats a hands-on view of a good installation...and spending a half-hour picking the brain of someone who's done this before.
At the MD/DC/VA meet, we sometimes have 7 or 8 cars there...all different makes and models of vehicles, all different levels of installation, all different types of computers, screens, input devices, etc.
There's no "right answer" when it comes to CarPC's. It depends on your needs and on your particular situation.
To answer your question about the audio...at least for ME...and my particular setup; I bought an Aux interface for my factory headunit...made by VaisTech. This gives me 2 dry AUX inputs to the stereo. I just ran a cable from the PC's Line-Out into the input on the Vais unit. Works well for me but, these devices only work on Toyota and Lexus cars. However, there are other manufacturers that make similar interfaces for various brands of cars. Unless you're driving something really obscure, it shouldn't be a problem.
That brings up another question you need to answer before you even start. Are you going to use the CarPC as an add-on to your factory stereo (as I did) or are you going to REPLACE your stereo with the CarPC? Again, there are pluses and minuses to both methods.
One final suggestion...fill out the information in your profile...as much info as you're willing to give. It would help if we knew where in the world you were (many folks here would be happy to meet you some time and show you what they've done, or...again...point you in the direction of a local upcoming meet.) It would also help if we knew what kind of car you drove...it's very possible that someone's driving the same kind of car and has already made installation mistakes and learned from them. The more we know, the more we can help you.