I may just be doing it wrong, but i'm filing some screw holes and cant get marine tex to fully fill them in. Can I thicken with micro balloons? What about a syringe?

Micro balloons might not work. What you need to make a paste is either Aerosil or Cabosil. The micro balloons will float to the surface. Aerosil and Cabosil are dessicants (fumed silica). It's what the crystals are in the packaging of electronic devices to absorb moisture and prevent it from damaging the electronics.

I use it to make fairing compound to fill in small steps that pose a problem for mat or roving when laying up fiberglass panels. You can make it to any consistency. We make it like a heavy grease so it stays where you put it.

Depending on where they are you might do just as well with a tube of Marine Silicone, or bath and shower silicone. They can be bought in small tubes with a nozzle. Ideal for plugging holes.

3M 5200 would work very well, but depending on where the holes are something more economical, like the aforementioned silicones, can be adequate.