The 'drag & drop', 'hit Apply' method is the correct way to award medals, qualifications in SH3 Commander.
As to which medals, quals, etc apply in-game, here is clarification from a previous post, courtesy of the mod designer:
"To summarise the Crew Manager component, as it seems to cause a lot of confusion:
-awarding *any* quals to officers impacts compartment efficiency as if they were awarded via SH3;
-awarding the *first* qual to an CWO impacts compartment efficiency as if awarded via SH3;
-awarding subsequent quals to an CWO, whilst being recognised in SH3, has no effect in SH3;
-awarding a qual to a PO impacts compartment efficiency as if awarded via SH3;
-awarding a qual to a seamen, whilst being recognised in SH3, has no effect in SH3;
-awarding the U-Boat War Badge has the same effect as if awarded via SH3;
-awarding any other medal, whilst being recognised in SH3, does not adjust resilience/morale/experience as it would if awarded via SH3;
-promotion/demotion, whilst being recognised in SH3, does not adjust resilience as it would if awarded via SH3 (although there is no demotion via SH3);
So a lot of what you can do in the Crew Manager *is* recognised and effective in SH3. It's really just the medals and some aspects of the qualifications that, despite being recognised in the game, are not effective in the game.
Now, whilst quals to seamen and extra quals to the CWO are not effective in SH3, they are still handy "markers". Also, I know of some people who believe that despite not being recognised towards compartment efficiency, SH3 tends to align these qualified seamen to their respective compartments, but I haven't tested that myself.
So, in summary, if you only want to award objects that mean something in SH3, don't promote (or demote), don't award EKs, DK or RK, and limit quals to 3 for officers and 1 for POs (note I'm silent on wound badges and front clasps as I have never been in a position to test and compare either). "
Hope this helps.
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