If you're grinding low level mobs for xmog items, I would make sure you babysit your bot as much as possible, just in case you get a whisper from a GM. Also, make sure you're not grinding on mobs that are used by lowbies for quests, because they can report you for doing that, and that could possibly lead to a ban. Just be sure that whatever low level mobs you're grinding on are out of the way and aren't used for any sort of quest. Also, I was more referring to grinding on mobs the same level as you, for leveling purposes. This is one of the more obvious botting techniques that will get you banned.
If that's the case, and you've had bans on your main account already, then I would suggest you not play your main while you bot. Try not to have your main account tied to to your second account in any way. Don't use the same email address, don't use the same payment method, don't use the same name, don't use the same IP address, etc. Try to make them both as different as physically possible from each other. That way, if one of the two does get looked into, Blizzard won't be able to tie them together, and you have a better chance of just one of them getting banned and not both. Now, keep in mind, that this is only a way to cut down on the risk of getting all accounts banned, not a complete preventative. It is still possible that they can get both of your accounts locked down.