Is there a smart way to bot in battlegrounds? Or do I just run the bot?

make sure you have a fight class for your class it makes the bot actual cast and stuff and also make sure you watch you bot i never leave my bot alone for more then a hour and even then i usually check on it ever 10-20 mins just to see if its stuck and what not

I STRONGLY recommend just using WRotation in BG's unless you have a laissez-faire attitude towards your account, or are watching the screen frequently - frankly, any high traffic area should always be supervised.

That's not to say WR is not reliable, actually it is remarkably so, but there are times where people can pull/push you off areas and it, like any automated program, can get a bit confused and that's when people notice.

WRotation allows you to gain the benefit of not having to smash 1,2,3 all the time whilst maintaining a human, fluid, control appearance on your character.

Plus it (WRotation) allows you to annoy all those Sub Rogues. :P Seriously, my damage from Backstab from BGs has been reduced SIGNIFICANTLY. It's hard to backstab something that's constantly facing you. You get to spend your whole concentration on ways to piss of random classes.