ATAC-seq peak annotation and downstream analysis
The way we do this (and I think its quite common?), is to merge all the files of the same condition (taking the same number of reads from each), and then calling peaks on the merged sample - so you would have two peak sets - one from normal and one from disease. You then do the union of the two peak sets. 

This makes annotation much easier.

For downstream quantitative analysis, you can then quantitate each individual sample against the merged peak set.