If it is an 'upgrade' version, then just overwrite MAMEWAH.EXE.
If it is an 'installer' version, I would recommend:
1) Backup the contents of your \MAMEWAH\Files folder (unless you want to reconfigure everything)
2) Un-install MAMEWAH using Control Panel > Add/Remove Programs
3) Install new MAMEWAH
4) Restore your backed-up files
Uninstalling before installing the new version will eliminate multiple entries in the Add/Remove Program list.
I recommended backing up and restoring files - note that some 'old' CFG files will NOT work with new MW versions. This recommendation is almost specific to the latest release, v0.963, which is compatible with the previous v0.962.
For MAME, I personally just overwrite MAME.EXE, and run 'mame -cc' again in case any new options have been added
