The CV64/3d is a two-piece card, if it has the ScanDoubler option. The SD goes in the Video slot, and the CV64 plugs into the Z3. There's no way to insert it wrong, provided you actually manage to insert the card without breaking anything. (Which is a challenge, as the card is BARELY able to fit in the slots -- installation takes about an hour, and that is if you know exactly what you are doing!)
The software install is VERY dodgy on the CV 64/3d, as well. I've never had an install go flawlessly. If possible, what you may want to do is try to snoopdos the loading, and make sure nothing obvious is failing (improper version or missing file).
Also, if you can, try loading the software on a bare workbench install (no patches or hacks) and see if you get better results.
You might also want to try Picasso 96 instead of the CGx software. Why not? nothing to lose, and it might prove your hardware is ok.
Personally, I wouldn't be TOO worried if the software didn't work right on the first try. It rarely does.