How to control the amount of epoxy used?

Alvsaurus,
When applying epoxy into holes to insert fiberglass rebar, the following has been my basic approach. First load the mixed epoxy into empty caulk tubes if it isn't already in tubes. Fill the hole approx. 75% and then twist the rebar into the center section of the 1/4"-3/8" oversized hole. Judging from the amount of overflow or void created on your first attempt try to fill the other holes with an amount necessary to achieve your goal. That goal may be flush or recessed so another type of epoxy or other product can be used to form a cap. The fiberglass rebar should be at least 1/2" shorter than the depth of the holes so there will be epoxy encapsulating the ends as well as the sides of the rebar.

You can tape/mask off the exposed perimeter of the hole if desired. This will help keep epoxy off the surrounding visible finished fabric. Caulk tube extensions can be applied to the tip. This is helpful if the hole is deep so you can start at the base of the hole and caulk outward. This is done by pulling back the tube as you gradually gun the epoxy, feeling just slight contact with the epoxy. A careful approach will keep the epoxy from surrounding the tip and possibly creating air pockets. A good sense of feel and focus is important, especially when working in blind areas. You can pull the gun back and gently push it forward to reset the contact point when needed. Try to visualize your location within the hole and how it is filling up. Completely filling the invisible portion of the hole and encapsulating the rebar is important for structural integrity.