The current software does not have a way to use a different EQ between the tuner and the MP3 player. The only differences in EQ are between car mode and home mode as described here.

The primary complaint about the tuner EQ is that it's got (by default) a bass-boost feature when playing FM radio. Also, the relative volume of FM/AM/MP3s tends to be different. This can be worked-around by using the custom Hijack kernel and inserting the following text into your config.ini:

[hijack]
disable_bassboost_FM=1
volume_boost_FM=-2
volume_boost_AM=-6
volume_boost_AUX=4