If you really want to be methodical about it, you'd want to scrutinize the analysis profiles for each malt for things like protein content and extract potential. But that still wouldn't tell you what kind of flavors and aromas you'd get from it.
More practically, with experience you just get a feel for it. In your example, I would want to substitute a German Munich malt for the Belgian Munich malt, because I know the two start with similar base malts and undergo similar processing. Generic "Munich Malt" from the LHBS could be an American malt, which may be a strong converter but made from a lower quality malt which would lack the flavor/aroma character I'd want.