I have read the documentation over many times and experimented with various mixes of filters, Legacy Mode, and free SQL.  I cannot figure out what is happening.  Changes get applied I don't want applied and changes I try to apply don't do anything.
Example:
I set default action to ignore (tried Automatic as well, not better)
Pasted some valid sql in the free sql field of a single item
Set filter to Free sql only and legacy mode to different settings
When I clicked Fix DB the sql didn't run and the core DB schema changed.
I may have figured out why sql didn't run (while typing this), but too tired to check at moment, but still need ideas there.  I knew that a component I just installed and propagated down through to my slave sites created a table (not a supported component for install). I was attempting to use the Maintenance tab to get the table created.  Not happening...
The rest of it, if I get errors when it checks the DB, WHAT am I supposed to DO about it?  What can the maintenance tab do and not do?  A use case would go along way in clearing this up.  Just stating what the various options mean isn't helping me.  I need to understand when they are applicable.
If this is just me, then please someone help out the poor idiot here.  I just need one, maybe two, situations walked through to a successful resolution.  From there I know I can extrapolate.
Thanks in advance