I presume you mean the side purflings....
Here is how I do it. When I bend my bindings I tape up the purflings for the sides in between the bindings. You have to tape every thing REALLY tight so the purfling strips don't buckle and get all wavy on you. (I guess it goes unsaid that i am using a Fox bender for this)
I DO NOT usually glue the purfs up to the bindings ahead of time.
After everything is bent, if the purfling strips are wavy in any spots I press them flat with a clothes iron on hot. This usually fixes any problems.
To route the channels I first route only the depth of the binding alone (not including the purf depth). This handles framing the end graft. Then I lower the cutter by the depth of the purfling and route again and go as close as I dare to the end graft without touching it.
I finish cutting the channel up to the end graft purflings by hand with chisels and razor blades.
Once that is done I mitre the pufling exposed in the end graft. Then I cut the matching mitre on the side purfs. Once I am satisfied and the purf lines up the way it should (the waist hits the right spot etc.) I tack it in place @ the end graft with a tiny dab of medium CA on a tooth pick. I take in in a couple of spots to hold it in place while I fit the binding.
After the bindings have all been cut and fitted I tape everything up and CA it in place. (Go easy with the glue and let it wick into the joint. Don't squirt it in -- that just makes a mess inside the guitar.
I have had pretty good luck with this.
