I'm sure it's possible, but I had a lot of problems getting it right (couldn't wrap my head around the mangle/QOS rules for dual-wan or it wouldn't work properly). Eventually landed up buying 2 hAP's - First one does strictly PPPoE, and the second one does the QoS. Basic diagram: LAN----hAP2(qos)----hAP1(multi-pppoe)----WWW. That way the QOS router thinks that there is only one 'WAN interface', when that wan interface (the other router) does the more complex routing and branching out
You can probably also accomplish a similar setup on ONE device if you use the Metarouter (virtualization) feature, but this overloads the CPU on the smaller SOHO Mikrotik devices I've tried it on. Easy to accomplish if you're just running your Mikrotik 'routers' as actual VM's, though.
There's probably a more elegant solution to the problem, but I've yet to find/work it out
Edit: Ah wait, I see that by 'balancing' you meant 'bonding', rather than 'QoS' - my bad. Haven't had much luck with bonding either myself, so hopefully someone else can contribute