Another option for the menu, although I'm not sure if it's available in the stable fluxbox, is a script by Han Boetes called fluxbox-generate_menu.
It basically scans your application directories for programs specified in the script, and builds a new ~/.fluxbox/menu automatically. It also adds a menuconfig file in which you can put some defaults...in your case you could use aterm with customized flags as $MY_TERM, and the menu will be generated using that aterm for all applications that require a terminal.
Alternately the menu script could be edited directly (as is my preference) to prevent overwriting an edited ~/.fluxbox/menu
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