Smartfade Control Software

I'm lighting designer at a high school and we happen to have a smartfade 2496 board and I have been using ETC's Smartsoft control software to control the stack from the PC.  However, the design for the show we are currently working on exceeds the capabilities of the Smartsoft program (so I think).  

Here is what I'm trying to do:  I have a group of lights in a specific area that are pulsing up and down at intervals.  While this is happening I have other cues that are happening while the lights are pulsing.  Now as far as I know standard Make-a-memory--add-it-to-the-stack process makes this idea nearly impossible.  If there was a way I could group the lights and make a loop of cues that would continue looping while other cues were called that would be perfect, however I don't know how to make Smartsoft do that.  

How do I get Smartsoft to do that if at all?  Secondly, is there another program out there that can talk to my board and get what I need to get done accomplished?  Keep in mind that I am at a high school and have next to no $$$

Thanks in advance! 

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