Hello Smikelz,
your photos from the UAV should come with a flight log containing the x,y and z values and they can be imported directly into Agisoft.
After you add the photos into agisoft, you can align the photos (workflow tab). then you build dense cloud, mesh then orthomosaic. Then you can export it as tif to be used in arcgis.
There are a few tutorials on Youtube to follow, or agisoft also has a manual that you can follow to create you orthomosaic.
good luck!
regards,
jessica