Glad your on your way. If you want to know what is possible if you just stick with Sketchup, have a look at my build parallel HEX (link in sig).
There are a few issues that I can see with your design, I hope you don't mind some constructive criticism:
1. The airflow looks woefully imbalanced and inadequate. You have a fan on the PSU which will be drawing down on it's components and effectively extracting out the back of the case.
2. I only see one other fan, presumably an intake. I'd want better airflow over the motherboard and rear of the graphics card.
3. Where does the radiator get it's cooler air from? I don't see any other vents or air holes near or opposite to it.
4. If the radiator is extracting, you're going to get a bit of a warm right leg.
5. Check the angle of the window the panel - it's difficult to tell from the images but I think the back edge (and possibly power cables) of the video card are fowling it.
6. Not sure how you intend to fix the panel with the window on it, but make easy to take off and put back on.
7. As you are watercooling it, be prepared for a bit of a ball ache when installing. It won't be easy to tilt your case to get any stubborn air bubbles out, and have you any thought about how you'll drain it?
8. I don't see any hard drives fitted.
9. Don't try and make your own motherboard rear IO mounting plate; buy a real cheap case and strip it/dremel it for one. A £20 quid case will save you a lot of grief.
10. You panels don't have any physical depth to them, unless you are intending to make the panels out out paper

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It's a lot of work for something that's going to be hidden under your desk, but go for it, you'll learn a lot.