I need to check and set the valves on my 1000ss, I was wondering what I will need to do this job.
In the manual it say's you need to use two dial gauges with ducati part fixture's.
Can I get away with one gauge and an alternate type of holder/fixture ?

Are you checking clearances or checking and adjusting cam timing? As far as I know, and I may be wrong, you only need dial indicators if you are adjusting cam timing. If you are checking and adjusting valve clearances all you need is a decent set of feeler guages.