I have a dual extruder Replicator 1 and a uPrint. As someone who uses both the short answer is that the Replicator 1 doesn't do support material the way you're used to with the Stratasys machine. There is a way to have support material generated if you use ReplicatorG, but it's breakaway support printed with the same material as the model (not the second extruder) and a major pain to deal with -- nothing like the soluble support that the uPrint offers. A few folks have experimented with PLA for support material but so far it's very experimental.
Having said that, I've found that with a bit of extra effort you can design in custom support material in your models that you can snap off. Obviously it depends highly on the design you're printing, but I've documented a bit of what I've been doing here:
http://atomsandelectrons.com/blog/2012/10/battling-gravity/
The benefit of the Stratasys is you can be totally lazy and not worry about printability. But as you've no doubt learned from using it, your print times go up massively when you use a lot of support material. Whenever it needs to switch materials it has to tilt the print head to the other extruder, clean the tip with the bush, etc. which burns time. So I find myself increasingly printing on the Makerbot with designed-in support if I can as it's faster and I can use more colors. The uPrint is always there when I don't want to risk a failed print or don't have the time to design in support -- sounds like you've got this backup option available too.
What I'm saying is you're not going to get the support material flexibility that you have with the uPrint, but if you're willing to invest some time learning the constraints of the machine you may discover you don't miss it as much as you might think.
-Chris