i have an rc10gt. what can i do to protect it from mud damage, or should i not run it in mud at all

I have used condoms w/ my mini t, so anything rubber like a tamiya rubber bag or a large balloon. put silicon grease in the end and close it tight w/ a zip tie

what about the engine-will the filter keep out everything?

it should be ok as long as you dont run for an extended amount of time where the filter absorbs water then the water goes into the motor.