I have two different ATAC-seq libraries that I wish to compare on a genome browser. I have used Macs to generate bedgraph files for each individual library using the command: 

macs2 callpeak -t macs2 callpeak -t bamfile --outdir /path/to/ -f BAMPE --keep-dup all --pvalue 1e-2 --call-summits --bdg

I then convert bdg to bigwig. 

How can I best normalise the two ATAC-seq libraries that I want to compare by library size? Can I do this in MACS? Or do I do it after I have generated the separate bdg files? 

Thank you, 
I never use these bedGraphs from macs2. They always look kind of weird (a very scientific statement, I know).
You can generate a read-per-million normalized bigwig with this command, using the latest deeptools version:

    bamCoverage --bam in.bam -o out_normalized.bigwig -bs 1 --normalizeUsing CPM -e