Should I merge all subtools before painting? Also after I have finished painting my piece how should I save it?
I suppose all depends on what your endgoal is with your model.
If you are staying within Zbrush. Just paint on each subtool, polypaint is kept for each subtool seperately.
If you do decide to merge for whatever reason, make sure you select “keep polygroups”. That way you can ctrl+alt click a part of your object which used to be a subtool and i’ll hide all the other parts of your model that used to be subtools. Making it still quite easy to pain without affecting the rest of your model.
Thank you. Is there any special way I need to save once its painted?
As before, if you plan on keeping all your work in Zbrush and not for an external package/renderer. Saving as a ZTL (ztool) will be fine, it retains Model/polypaint/material.