put your custom stuff (not maps) .pk3's in a folder other than /baseoa (for example, i use /OACTF) and then start your server with command like this:
./oa_ded.i386 +set fs_basepath /var/oa/openarena-0.8.1/ +set fs_game OACTF +set dedicated 2
also, make sure your webserver has that folder available to http requests.