Get the sound you want out of the amp first, then record it and tweak the EQ on your amp until it sounds good on recording...sometimes it can sound good out of the amp but not on recording...
Sometimes lowering the bass a lot, and raising the mids to about 7, and the treble to about 5 or 6 can help, it depends on the amp/guitar. For example, Van Halen is known to use really high mids on his leads. Some amps just sound muddy with high mids though.
Also mic placement is really important when mic'ing an amp, you could have all the right settings already but the mic placement could be messing up the sound. Your room also plays a role, but not so much with an amp as with an acoustic instrument.
I'm assuming you're using a mic, if you're recording direct then that's completely different.