So, a place to get started if you're dead set on doing this in a single command from the command line:
cat corpus.txt | tee `stanfordNER -options here > out1.xml` | myNERTagger -options here > out2.xml && diff out1.xml out2.xml | awk to do whatever merging you want here...
But what you'll likely find is that this is not a solution. You're going to want to go sentence-by-sentence in a little script, calling pyner or similar to hook into the Stanford tagger and then whatever custom tagger you've built, merging the differences as you go along. The output formatting of your taggers will change how this looks pretty dramatically.