One consideration is the amount of overlap you're looking for. Default behavior will take any amount of overlap. You can change this to require a greater amount or to allow a gap between the peaks.

I prefer a stricter threshold for overlapping peaks, where in this case you might require at least 25-50% of the ATAC peak is overlapped.

Also with bedtools pay attention to what you are outputting. In general, if you provide the ATAC-peaks as -a and K27ac as -b then the output will be the original ATAC-peaks that are marked by K27ac. I imagine this is your desired output, but if you wanted to see K27ac peaks that contained accessible regions, then you would input the K27ac peaks as -a.

Also, the default behavior is to output a line from -a for every overlap found in -b. Sometimes this isn't really an issue, but for example if you had a really large ATAC peaks covered by two separate K27ac peaks (assuming ATAC peaks are input as -a), then you would get the same ATAC-seq peak twice in the output file. I usually use the -u flag to keep a one line per peak ratio.

This is all obvious in their documentation which is comprehensive, and sorry if it's all obvious to you, but it wasn't obvious to me originally.