Getting the scores scanned and onto your iPad is not really an iPad thing. That is more of a regular computer situation. You must find a good scanner that is quick and handles larger than 8.5×11 paper.
Luckily school has a Minolta biz hub copier that scans very well! The first year I was using the iPad I simply used my plain old home style printer/scanner. I have found that Staples has a Brother copier that does large sheets like my concert band scores that I am thinking about buying. You need a scanner that has a feeding tray and will do double sided scans.
Once I get the music scanned though my workflow is easy. All the scans are saved as PDF files and out into DropBox. From DropBox I then use either ForScore or UnRealBook on the iPad for the PDF music. Both these apps have their strengths and they are only about $5 each so it is silly not to have both. It also gives you a backup if for some reason one doesn’t work all of a sudden. When y are asking about technology you must always have a backup plan! I’ve never had an issue with either app though in the past here years.
Another important point is that Both of those apps are written by musicians, for musicians. I was using GoodReader for the first couple of months and there are needs we have as musicians that GoodReader doesn’t fill.
After I am done with my current PDF files I then back them up in a folder on my computer and also on Box.net – I use Box because I was able to get 50 GB’s during a promotion they were running. The idea is simple though…. Get them out of DropBox and free space up for current needs as well as having backups!
If you will be specific about what exactly you are having issues with I can give you more ideas.