I had a mold remedy company out to remove a 4x5 section of dry wall in my garage and clean the mold. The company said they could not know exactly what this would entail before doing this first step. They gave me a written estimate for 5 hours of work, going into the interior behind my cabinets, apply fans, and clean the mold for $1159. I accepted the estimate for these time and materials parameters.

The job ended up smaller than the estimate. The company spent 1 hour removing the drywall and treating only exterior mold at the base of the wall (5 linear ft). Nothing interior and no fans.

The company sent me an invoice for the full $1159. I documented that the actual work was much less than (1/5) than the estimate and sent them a check for $300 (Paid in Full). Its been two weeks and have not heard back from them.

What is the best way to handle this dispute and what should I be doing right now ?

You got an estimate of $1159 for the job, assuming they don't find undetected significant problems... you didn't get an estimate of $231.80 per hour of work, and they charged you for 5 hours but didn't do the 5
. If the job ran a little over they would have bought that themselves... if it ran less they don't owe it back to you either. That's how it works if you aren't being billed by the hour, but by the job.

You are going to lose if you try and fight it.

They may not have contacted you yet because they are giving you time to pay the rest.

I accepted the estimate for these time and materials parameters.
Was this a 'time and material not to exceed' situation? Curious if it was presented as a hard quote, or a 'time and material' job. (I just find it interesting that you use the phrase 'time and material'... )

Did you have a written contract? Did you sign the estimate form?
What did you ask them for when you first contacted that company?
If you asked them something like- how much will it cost to remove this mold?, and they gave you a written estimate of $1,159, they did what you asked them to do.
On large contract work, it is called different site conditions.
If they had found damaged studs, mold on back of drywall from adjoining room, etc and had to replace some structure (even with a contract), they would have requested additional compensation.
If you asked for mold removal and they did mold removal and there is no written contract containing other detailed requirements, I think you will be held responsible for paying the estimated amount. But, I would not deal with this company again, for sure. They could just as easily have given you a break.
Most states have contractor licensing boards and consumer protection divisions in their Attorney general offices. Make some calls. You might find that the estimate you were provided does not comply with the laws for your jurisdiction. Your contractor accomplished a windfall (so far).

what should I be doing right now ?

Wait and see what happpens, which will probably be nothing.