The four User Banks (U1-U4) are an exact copy of the four Factory Banks (F1-F4) when you purchase the Rev2 new. You can only save over patches in the User Banks... the factory banks are your permanent backups of the originals.
(Note: there are actually ways to overwrite factory patches via more advanced means (sysex), if you use up all your user patches and need more room in the future, but you've 512 user slots to work with... so, not a problem for most.
But, yeah, just edit and write to the U1-U4 banks and you should be set.