It is a good idea, the quality is getting better, but there is always something that needs to be tweeked on them, to make them run smoother and quite.
On the gear boxes I use 3 D-cell Batteries and I have a spare set of Heng long motors that I mount into the gear box that I am breaking in. If you don't have an extra set you can use the motors that come with the gearbox, but make sure they are covered so you don't get goop in them.
For the removal of the fine bumps in the gears teeth, I like to use good old hand mechanics had wash with pumice! Not a ton, just enough to coat all the gears and then I let it run for about 3 hours in each direction. The cross bars for the gear box may need to be tightened or loosen to make you gear box run freely and then I lock the screws with Loctite.
Then I clean it off with W-D40 and I will lubricate them lightly with white lithium grease. It is a good lubricant and will not fly all over the place, but on certain tanks were I need the gearbox heavily lubed I use good old 3in1 oil and make sure I have cover on the gearbox!
Here are a few pictures of how and what I use to break in the metal Gear box, those motors are my break in motors, I broke in your motors separately for about 90 minutes in each direction.
Download a copy of this document Motor Break-In Procedure.doc here