I agree with Jeff that when you try to play a bass part on guitar, it has the tendency to come out like a guitar riff if you're not careful. Especially when you're trying to feel out or jam a bass part from scratch. There's something about having that guitar in your hand that makes you think like a guitarist (amazingly enough!). It works better if you can pretty much hear the bass part in your head first, then it's a matter of translating it to guitar.
However, another Melodyne method that might work better for you is to hum the part into a mic and then have Melodyne convert that to MIDI. It's probably somewhat easier to get into that bass player "mindspace" when you're making bass noises with your mouth as opposed to trying to play a bass part on guitar.
I have a crappy Logitech USB mic set up for quick and easy humming into Melodyne. You don't need high fidelity.