Once you filter for mate-pairs mapping to targeted regions, the mate-pairs that do not overlap are already removed. If you post an example of what you have and what you want, I can help you more.

With the -type parameter of pairToBed and -v of intersectBed, you can definitely achieve it, but can't pinpoint without a snippet of data.

-type     Approach to reporting overlaps between BEDPE and BED.

    either    Report overlaps if either end of A overlaps B.
        - Default.
    neither    Report A if neither end of A overlaps B.
    both    Report overlaps if both ends of A overlap  B.
    xor    Report overlaps if one and only one end of A overlaps B.
    notboth    Report overlaps if neither end or one and only one 
        end of A overlap B.  That is, xor + neither.

    ispan    Report overlaps between [end1, start2] of A and B.
        - Note: If chrom1 <> chrom2, entry is ignored.

    ospan    Report overlaps between [start1, end2] of A and B.
        - Note: If chrom1 <> chrom2, entry is ignored.

    notispan    Report A if ispan of A doesn't overlap B.
            - Note: If chrom1 <> chrom2, entry is ignored.

    notospan    Report A if ospan of A doesn't overlap B.
            - Note: If chrom1 <> chrom2, entry is ignored.