I know how to chart lead and bass, but what song track do you select to do rhythm? Is it Part Rhythm or is it something else?

You can author it in any of the real guitar or real bass tracks, just use "Track>Rocksmith>Arrangement type>Combo" to designate the track's arrangement type.

After I select that, how do I put the rhythm guitar in there with it?

@@MissingElements - As @@raynebc said, you can put the "Real" tracks in EoF (Guitar, Bass, Guitar_22, or Bass_22) into the Toolkit as any arrangement type you like. If you want one of the arrangements to be the rhythm guitar, load the .xml into the Toolkit, then set "Type" to "Guitar" and "Name" to "Rhythm" (you can also do "Combo" and then click the "Rhythm" button under "Gameplay Path". All that matters is at the end of the day you have the "Gameplay Path" as rhythm.

 

Depending on what's in the song (only rhythm guitar, extra rhythm/lead guitars, 5- or 6-string bass), I've set all of the "Real" tracks in EoF as rhythm guitar parts successfully.

I think I kinda understand this now. I'll find out at the end if I did it right or not. Thank you guys.