You should really change the filter and use a pump when doing an auto trans flush. Without the pump, youre only going to get like 2/3 of the old fluid out...and really, whats the point then? This is why shops charge nearly $100 for this job...personally, I think its worth it, since it includes the fluid, filter, and labor.
It isnt really oil, so you cannot put it with regular oil...call a few shops and see if they'll take it.