If you don't build in any gaps you won't have to fill them. I have tried several different binding materials and glues and have settled on the following - it seems to work for wood, plastic, any kind of purfling.
Seal the top with a coat of shellac. Route the binding and purfling channels (think about the order so you have best support of the router and bit). Clean up the channels so they are perfect. That means the corners are square and there aren't any little fuzzies.
Put the binding + purfling sandwich in the channels and tape in place (include the teflon strip if you are doing pearl). I use low tack 1 inch masking tape with gaps about 1/2 between pieces. Get the miters and end piece and everything else perfect. Make sure the binding and purfling fit the channel pefectly. Push against it with a little block of wood, if it moves it isn't perfect. Take it out and fix it.
I want the binding and pufling to stand proud of the top and sides by a couple of thou - you can feel it but hardly see it. I want to be scraping binding back to wood, not the other way around. I'll frequently use a quick clamp at the waist and its often necessary to come up with creative clamping at cutaway horns or around headstock. The goal is the same, you want the binding perfectly tight.
I then put a tiny drop of thin (#10) CA on the binding and purfling between each piece of tape with a pipette. The idea is to put the drop on the sandwich right up to the top but not actually get any on the top wood. It will wick right down between the layers of the sandwich and tightly tack everything to the guitar. If there was any movement with the wood block I'll hold that part of the binding tight while the CA kicks off. I don't use accellerator because I think it can stain the top.
Once the CA has completely kicked pull all the tape and with the pipette run a bead of CA over the entire length and width of the sandwich. Again, the goal is to get it right to the edge but not go over. Tip the guitar on its side and run a bead on the bottom of the binding.
After that has kicked off, scrape back the binding and purfling to the top and sides - you will be removing the glue that was sitting on the top and leaving just the wood and fiber. I make it a point if I do any sanding to always scrape afterwards - you will get a much nicer line with your different colors.
Once in a very great while I will get a tiny gap - they usually don't show up until I'm finishing. Its pretty easy to drop fill with lacquer at that point.
Here is an example - prebent wood binding for an archtop (I bent a couple of extra pieces so I could pick the best one) - these are commercial strips that you can buy from LMII
Binding in place with one ebony purfling line
Head, neck, pickguard and f-holes bound to match
I simply could not have done some of this (f-holes) with something like Titebond
thanks for the tips guys. Great advice 