Multiple rom paths can be used in mame and arcadeos. However you have to set them and since I don't use them I am not sure of the exact setup. Take a look at both mame and arcadeos docs for the proper way to do it. Arcadeos 2.5 will has a bit of new info on setting multiple rom paths when filtering. I quote it direct from the docs.
Quote
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Multiple ROM Folder Filtering:
To use multiple ROM directories with Custom Sets, divide roms into
desired directories. List these directories in rom path line of the mame
config file seperater by semi-colons (

. Within ArcadeOS, set "C.List
is Copy" and "Filters Active" in the ArcadeOS Config:Information menu.
Proceed to the ArcadeOS Config:Filters menu and select the position of
the desired ROM directory from 1 to 10 (0=not filtered). Repeat this
Filter setting from within each Custom Set. All other filter options may
be used with this setting.
End Quote
BobA