I am replacing bearings in my sx bottom end, should i leave the seals on both sides of the bearings or remove inner seal and ca glue outer seal?

Keep BOTH seals and CA the outer one.
Pending on AGE of the SX bottom end, new engines also use a brass seal plate between bearings

Thanks Scott, it is one of the older ones with the divider cast into it. Will the bearings get enough oil with both the seals in there?

You should be fine, but can add the seal plates between the web and outboard bearings easy enough.
Only effect is on PTO end you may need to shorten drive collet thickness of the seal plate installed ?