Prefixes

This may be a stupid question. But I have no idea.
I'm trying to find out why it's uncomfortable not incomfortable.
The prefix un meaning NOT
The prefix in meaning NOT
If they mean the same why are they not used with the same words?

Please help me.
It's driving me crazy!!
CaN'T sLeEp.......

[Francois]

I believe you just have to learn them by heart.

FRC

[Tdol]

It is unfortunate that we have so many negative prefixes and there are really very few rules. There are some, like il- before words beginning with 'l', but even these are not consistent. Francois is right- it's a question of listening, reading and learning.