How do I pour concrete over basement plumbing?
I am perplexed to how the plumber would have glued the drain down before concrete was poured.  If he really do this you need to get a new plumber, seriously.  Let's just say he didn't.  If my plumber was doing a job for me he would leave the pan in the same condition, albeit not glued in - since he is double checking the location, especially for fixed pans.  So try to pull it up (if it is glued and you can pull it up, well it shouldn't).
This is just a comment.  Based on the picture it looks like you could have plumbing traveling uphill, if this isn't for venting that isn't good.  
To fill your holes you need sand then aggregate (small gravel) and then you pour your concrete.  You will be pouring a little over existing floor but not much and feather flat.