I normally prefer to use the Hunspell spell checker in Trados Studio: I can set the various parameters from within Studio (instead of having to change them in MS Word), and I don't mind that Hunspell normally flags more false positives - I actually prefer that to MS's sometimes more permissive approach.
There are, however, times when you need to change the spell checker used - for instance, if the language version used in a project is not supported by your default spell checker.
This happened to me in a recent project: the customer had set it as English to Italian (Switzerland), instead of the normal Italian (Italy). Hunspell does not have a spell checker for Italian (Switzerland), so Studio was not performing any spell checking at all - if you selected the Tools menu you would see the spell-checker option grayed out.
In such instances the workaround is simple: just go to Tools > Options > Editor > Spelling, and select the other spell checker.
In my case, I switched from Hunspell to MS Word's, and I was able to check my project. In other instances you may try the reverse (selecting Hunspell when you normally use the MS Word spell-checker). This is useful, for instance, if your installation of MS Office does not come with the spell-checker for a certain language.