EXCEPT FOR means “with the exception of” or “excluding.”

We all ate meat except for Susan.
EXCEPT THAT means “except for the fact that” or “apart from the fact that.”

Your house is nice, except that it's a bit far from the station.
You can often omit FOR or THAT. But remember:

If EXCEPT FOR is followed by a preposition, always omit FOR:

I like dancing anywhere, except in noisy discos.
If EXCEPT FOR is followed by a verb, don't omit FOR:

Kevin was fine except for feeling a bit tired.