If I have a number of DC-DC converters as well as a local ground and an isolated ground, do I need a power flag for each output of a DC converter as well as one power flag for the isolated ground and a power flag for the local ground? Thanks in advance!
You could try and run the ERC tool and see if you get the dreaded error. 
power flags are different to power labels. A power flag tells kicad that some net is powered if there is no other pin on it that does this already. (Example needed for when you use a generic connector to power your board)
So every net needs at most one power flag.
Further reading:
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