Why not put you a loop in the script that cycles between pools? that way if the cgminer crashes or loses connection then it will auto resume.
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"Cycling" the pools makes no difference unless the problem is your internet - in which case you should find it can't connect to any pools.
When you restart cgminer it will simply connect to whatever pool is available and supplying work, in order of the list supplied.
If the 1st one wont respond, it will connect to the 2nd one etc.
All (reputable) standalone miners have a crontab entry checking the API every few minutes that restarts cgminer when it isn't mining.