Dan,
At the moment, yes, you are going to see all of the individual pieces. There is one piece missing in MobileSheetsPro to be able to help you filter out instruments you don't want to see - the ability to either populate metadata from the filename using a matching format string, or the ability to create multiple versions of one song with a different instrument in each (and a switch to change which instrument you want to see which would drive which version is automatically selected). I have solutions for both of those planned, but at the moment, you would have to manually edit each song and assign a piece of metadata you could filter on. For example, if you use custom group for instrument (or source type), you could then edit each song under a piece and add the instrument for that particular song/PDF. Then if you just filter on instrument using the dropdown in the filter bar, and your library would only show songs/PDFs for that particular instrument. I do apologize that I don't have a better solution in place for handling this at the moment, as I realize that is going to be tedious and a fair amount of work if you have a large number of PDFs. Having said that, if you have uniquely named all of your songs to include instrument in the title, there are a few tricks you can use to speed this up:
1) Type in the instrument in the filter box at the top. Only songs with that instrument in their title should be shown. You can tap the dropdown next to the search bar and limit it to title if the instrument name might show up in any other piece of metadata and you want to be explicit.
2) Long press one to start selection mode, tap the select all button in the floating toolbar at the bottom right, then tap "Edit Songs" at the top of the screen
3) Add a piece of metadata to uniquely identify them all (i.e. source/custom group/etc)
4) Tap OK to save the changes
This obviously depends upon your songs being named a certain way, but if you are lucky enough to have them all named in such a way that you can filter on them all quickly, then this shouldn't take you very long to fix at all.
Mike