If your layout is permanent I do what Shinkansen said, clamp them together and drill and bolt, they will never move. Stay away from the pattern maker dowels it is very hard to align them perfectly.
I now use hardwood dowels and drill the frames with a boring machine, that gives me perfect alignment every time. My old exhibition baseboard had them and they never wore down after a year and a half of constant use.
If your planning to take it apart the odd time, clamp the frame then drill 8mm holes and fit hardwood dowels, then drill and bolt them together.