About a year ago, I did a spreadsheet laying out the percentages paid for all the ones I knew about at the time--schoolpop, schoolshare, schoolcash, boxtops4education, igive. I haven't had a chance to update it, but I think it's a worthwhile exercise to do to get a feel for what companies participate and how much is paid. I would definitely recommend that you pick one and go for it--it's too confusing to have more than one, and most people won't take the time to go back and forth and figure out which one pays you the highest percentage.
Schoolcash no longer exists--it was just bought by schoolpop. I was bummed, because I used schoolcash a lot--their reporting seemed faster than schoolpop, and many of their percentages were quite a bit higher than anyone else's (except schoolshare). The purchase just happened, so it will be interesting to see if schoolpop keeps their lower percentages, or gets to take on schoolcash's deals.
The primary online mall used by my school is iGive.com. It has the most stores (400+) by a large margin, but also (generally) the lowest percentages. So why do we use them? The referral bonuses. They've had a $5 referral deal going on for about a year that has worked very well for us. Plus they have a program you can load that reminds you that a site is an "iGive" site, so we thought it would help people increase their utilization (no way of knowing if it really has). We've publicized it pretty heavily, but in a school of 750 or so, we'll probably end up taking in less than $400 this year, and that's from a very small number of users who do a lot of internet shopping. We've found that it's very difficult to get people to go through one of these portals, even though it usually requires next to no effort from them; they just don't think about it. But once they do it once, they tend to remember and think about it again. Next year, we're thinking about doing some online demos at the open house or at a nighttime event or something. And we may switch to publicizing another online mall, especially if the iGive referral program expires soon like they say it will.
Someone else here has had success using heartof.com, but I've never used them or looked into them at all.