You can use bedops to do the merging and bedmap to get a list of peaks that overlap the merged regions:

$ bedops --merge A.bed B.bed C.bed ... > merge.bed
$ bedops --everything A.bed B.bed C.bed ... > union.bed
$ bedmap --echo --echo-map merge.bed union.bed > answer.bed

Or as a one-liner:

$ bedmap --echo --echo-map <(bedops --merge A.bed B.bed C.bed ...) <(bedops --everything A.bed B.bed C.bed ...) > answer.bed

1. You can use bedtools intersect
2. It should not matter much.

You may want to consider using Fseq to call ATAC seq peaks instead of MACS2. H3K27ac gives fairly punctate peaks, so you should probably be fine, but any time you are doing intersections you should consider the size of the peak regions from both sets, and decide if how you want to define the peak boundaries for the intersected set.