Is it better to glass the sides after the fillets are done and taped?
YES .........
Fillet the seams and then glass the boat................
If you run a fillet of epoxy and wood flour alone the seams it is not necessary to tape them and it will make it easier for you when you glass the inside of the boat.
The fillet fills in the seam letting the glass lay on the area better then having a 90 degree crease in the glass at the seams.
If you want extra protection on the outside wear areas then tape the outside seams before you glass them of just forget the tape and glass the outside.
Usually folks that only tape the seams do not completely glass the boat.
Any thoughts on weather or not to glass the insides of the side pieces before final assembly?
Some folks have epoxied and glassed the bottom and sides before assembling them , they say it is a lot harder to bend the pieces when they do that but it makes for a good glassing job.
When I fillet a seam I paint the seam with epoxy and about 1 1/2 inches on each side of the seam. The reason for this is that I let the epoxy dry and then when I place my tape it is normally a 1/4 to 1/2 of an inch on each side of the seam. That epoxy I painted on the sides is where the tape goes and when I pull the tape it does not pull any wood with it since it is applied to the epoxied area and not bare wood.
Keep checking the fillet to make sure it is cured enough to pull the tape and not set up all the way or you will have the tape as part of the fillet , usually 45 minutes to an hour is when I pull mine , the time varies with the temperature outside , hotter weather the epoxy sets up quicker.
After pulling the tape you might have a sharp edge on the fillet sticking up , a rag bunched up with some acetone on it can be brushed
very lightly over it to smooth it out