If you want to use pedals in the loops of the Lynch Box (I guess this is the Line Level loops you are referring too) you can. You just need to use something to bring the loops to line level. I used a EBTech Line Level Shifter LL2 :
http://www.ebtechaudio.com/llsdes.html , got it on eBay for like $60 Put it in the loop you want to use and hook the pedals up to it, that's it! I used a Boss DD6 and a Cheapie Chorus in the loop of the Lynch Box with it no problems.