Cream cheese flan recipes seem to all call for a blender: you just put all the ingredients (possibly minus the evaporated milk) into the blender, kind of willy-nilly, and whizz it up.  Problem is, I don't own a blender. Obviously, wildly throwing together all the ingredients ain't gonna work in a mixer. But what will? For reference, the ingredients I'm working with are 1 package cream cheese, 5 eggs, 1 can sweetened condensed milk, 1 can evaporated milk, and vanilla.   I know (from experience) that the cream cheese must be fully softened — otherwise you end up with a curdled mess.  Should I beat the eggs separately? What order should I mix things in? If this were cheesecake, I'd cream the cheese and sugar, but here the sugar is already dissolved in the condensed milk.  
This is very common. What you are describing would usually be called either a bain marie or a double boiler. It is normally used for things that you don't want to overheat, such as hollandaise sauce, ganache, and some other dairy based sauces.   As for advantages and disadvantages, it really depends on what you're heating. For the sauces mentioned above, the advantage is ensuring that no part of the sauce will get above 212F, the temperature of the boiling water. Microwaving will be faster for most things though. 