If I understand what you are saying...
With the Looper in the 'Post' position, you are recording the effected signal. If the looper is 'Pre' then you are recording the clean signal from your guitar and playing it back through the effects and amp that you have currently selected.
Therefore, for most jamming purposes, you want the looper to be Post. In that way, you can record a 'backing track' part into your looper using one preset and then change to another for your lead, without the 'backing track' changing.
I think you guys using the looper could find this diuscussion of mine helpful: