I just started dual boxing but what ive noticed is some ppl may also whisper my second toon. I solve this by using the pause function in keyclone. and also i use the addon twobox toolkit which has an option of routing your tells from your alts to whomever u want (my main). they may think its weird that i respond back from the main but no matters its usually ppl curious about the duel boxing.

so to answer your question:

to stop other clones from responding/talking gibberish, use something that pauses the broadcast on those keys (saves from having to redo all the keys, also remember keyclone ftw)

and good way to manage ur tells/following etc is an addon called twobox toolkit.

good luck to u