I have a Alesis SR16, what a great piece of kit and I am doing exactly what you want by using a dual pedal footswitch. The footswitch will stop start the drums and the B button will add a fill followed by a differnt variation. These things used are very cheap and ebay has loads of them. I use a Boss FS-6 dual foot switch but you can use two singles of any make.
Here is me jamming with the drum machine you should be able to hear the two patterns and the fill that is uses to in between A&B pattern. Apologies for my inexperience on the axe though:
My 1st Jam Session and Solo