Wondering how I can go about outputting the following command which would have the chromosome map already applied? So for instance instead of "chromosome # 26" representing the X, it is already changed in the binding matrix following counting, or is this only possible in post-processing (e.g. editing the csv output)? Thanks!

ChIP_count$binding

You can use dba.peakset() with bRetrieve=TRUE. This will return the binding matrix with the chromosome names in it. By default this is returned as a GRanges object; if you set DataType=DBA_DATA_FRAME it will return a dataframe.