Rob gives some good advice, but as often there not a right and wrong way to do these things, just a way that suits you best.
My own method is to paint anything that not the hull colour while still on the sprue, I cut as many of the attachment points as I can, trying to leave only one. I am not sure what sort of weathering your doing aside from dry brushing, I am guessing this might come after you have a few kits under your belt. But I would also weather the tools while on the sprue, namely chipping on the metal and what ever you want to do on the wood.
I then add my tools after the model is painted dry brushed and I have done any washes. If your using standard model glue, then you will want to remove the paint where they go, I think masking where the tools will go is more effort than its worth. You could use CA but many use a weld rather than glue. I use an old fine brush to apply mine and just apply it to the join between tool and vehicle.
Some people apply things like road wheels and tracks to the model before painting, but again I do these prior to fitting them.
My advice would be to try what seems right for you, and then maybe next time try another method and then decide which you like best.
I am a Norfolk man and i glory in being so
On the bench: Airfix 1/72nd Harrier GR.3/Fujimi 1/72nd Ju 87D-3