So I need to know definitively from someone if you can run a 3s and a 2s in series to get 5s??? I've read yes and I've read no. Has anyone done this before and is there anything special I need to know.

Before anyone says just go buy a 5s, my charger will only handle up to 3s and batteries and a charger aren't really on the budget right now.

Yes you can.

You will need to balance them separately.

Yes, but you will want to charge and balance them seperately, also would be best if they are of similar mah capacity. Using batteries of different capacity could result in over discharging the lower capacity pack.

I would state that much more strongly: It is almost necessary that they be the same capacity unless you have the discipline to strictly limit your runtime to assure that the lower capacity battery is not over-discharged.

An alternative is to get a low battery alarm and put it on the lower capacity battery.

Yes you can. I prefer to make sure the batteries are from the same manufacturer, same discharge rates, and same mah rating

+1 on that, the same specs from different manufactures will not always be the same in real world.

Also be mindful of the fact that the batteries will deteriorate at different rates over their lifespan. Using two batteries from the same manufacturer that have the same discharge characteristics and mah rating is the safest way to go, but monitor each battery's capacity periodically to make sure one isn't falling off faster than the other.