AFAIK, that 50a shunt is only good for monitoring the mega watt's amp output. If you're looking to monitor the battery bank, you may need to use a 500a shunt. They usually have 3/8" bolts, so you would just connect a short heavy cable from bank neg to one shunt post/bolt, and ALL other negs to the other shunt post. All other negs would include all loads, as well as the charger's neg cable. This way everything, in or out, will be monitored.
Page 7 of this manual shows how it's done with a Trimetric. Page 8 explains the wiring from shunt to meter:
http://www.bogartengineering.com/sites/default/files/docs/TM-2025Install%20Instructions9-12.pdfCan you post a link to the meter and shunt you have now?
thanks