Bontrager Tubeless Wheelset Question

I recently upgraded my current wheelset (Bontrager Select Disc) with a new set of Bontrager Race Lite Disc (tubeless compatible). I setup the wheels with discs, a cassette, etc...and decided to mount an existing pair of WTB EpicWolf Race tires to the rims with tubes. I did not use normal rim strips as these wheels have a plastic lining (which I assume if for going tubeless) and after mounting the tires, there are few spots where a few inches in length of the tire bead is seated too deeply into the rim so the tire is not centered on the rim. When I spin the rim, the tire appears to wobble because it's not centered. I checked the wheels and they are "true". I tried re-mounting the tires and it still happened in one spot, and I heard another spot "pop out" as I was inflating them. The tires are almost new, and are difficult to put on so that may be why they seem to sit so far below the edge of the rim in a spot or two. Would a rim strip help? Anyone else experience this or does anyone have any ideas on how to fix this? I want to stay with tubed clinchers, so please let me know what I can do. Thanks!!