"For merging the missions together, is this done in SiteScan or AGOL?"
Merging Missions is done within SiteScan.
As a side note, if you ever want to create a copy of a mission, you can Merge only the existing mission into a new mission.
"I can create and export tile caches from SiteScan into AGOL? or do I export merged missions as tiffs and then create the tile caches in AGOL?"
Yes, you can create a tile cache from Site Scan right into AGOL. You'll want to use the "Share to ArcGIS Online" tool that I described above.