The best advice I can give you is to get comfortable in your TT position. Not comfortable in an "I could ride like this for hours" sense, but comfortable as in "I can hold my body in the most aero position and still generate as much power as possible" sense.
This is especially important if you're gonna be doing a longer TT (20-40K as opposed to the usual omnium/stage race 3-6 miler).
I naturally like to nose ride- I find myself doing it any time I want to haul a**, so I actually enjoy a TT setup where I'm perched on the nose of the saddle and right on top of my pedals. My best riding buddy, though, likes to sit back on his seatbones and stretch out. He has to really "force" himself into position for a good TT, so he practices the position a lot more so that he doesn't feel awkward & off balance when he's in the aero bars & rolled forward on his saddle. Unless you've got mis-alignment problems and you're riding for hours at a time in that position, the patella thing really isn't that big of an issue.
Good luck!
Oh yeah- and you can apply for what's called a "morphalogical exception" for the seat over the BB thing. I will have to in the future- even on my road bike, the build of my legs warrants the nose being directly over the BB. They mention it in an article on slowtwitch.com: TT position for the UCI Challenged



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remember you don't have to spend big. We got me a Giant TCR2 which is a mid-range cost, and slightly aero frame. Slowly we have altered it to a more TT profile... picking up components on TradeMe (NZ version of EBay)... a bladed stem, tri-spoke wheels, bar-end shifters. We cut down old drop bars and turned them into bull horns and after a couple of attempts found the right aero bars to attach. 