Have you looked into any tutorials/videos on using the Pen Tool? Maybe if you find ones that kind of make you 'follow along' they might help you understand it's ins-and-outs.
For me personally, I've been playing with letter forms for so long that I can pretty much figure out where the nodes need to be to get the curve I want. But I go back to when everything, and I mean everything, had to be hand drawn so I've got a pretty good handle on letter shapes. But really, all a letter is is just another shape. I found out early on in my sign career that once I could effectively letter backwards (reverse lettering on the inside of windows) and/or upside down that it really didn't matter what the letter was...it was just a shape to reproduce.
Hang in there and keep practicing...you'll get it eventually. Using the pen Tool isn't really all that difficult, you just need to keep at it until you have your 'ah ha!' moment. After that, it will all seem so simple you'll wonder what the problem was before.
