I can't really understand when I should use one flag or the other, for example on this question.
Both of those flags seem to imply that a question is poorly written and should be removed, so why are they 2 different flags? Or am I missing something? I tried looking at How do I flag correctly? on the meta site but it didn't really help (the flags are now different?).
The flags have not changed, but the answer there focusses mainly on answers and doesn't seem to consider the case you mention, flagging to close (when you earn the close / reopen voting privilege this will redirect to the closing dialog).
However, it tells you exactly when to use the very low quality flag:
VLQ should only be used for things that are so hopelessly awful, they can't be fixed. When thinking about whether you should flag something as VLQ, ask yourself this question: If I could, would I just delete this immediately, or can it be fixed?. If the answer to the question is yes, I would delete this and no it is impossible to fix, then you might want to cast a VLQ flag.
If, however, the post could conceivably be fixed and might contain some useful information, then please do not flag it. Instead, either fix it yourself or, if that's not an option, downvote it.
In practice, I think this flag is pretty redundant, because on answers the not an answer flag is perfectly applicable to unsalvageable nonsense, and on questions, reviewers of the low quality posts queue, where questions flagged very low quality or should be closed are all sent, reviewers only have the option to close them, not delete them. Presumably mods can just delete them, or at least close and delete them instantly, so perhaps that is a reason why the VLQ flag is better than should be closed --> unclear for unsalvageable nonsense, but I doubt it makes much difference. Perhaps worth noting here that on this site ~95% of closures are done by the community, not by mods.
There is also a bug feature of the VLQ flag which is... not always desirable, which is that when it is resolved as helpful, a downvote is automatically cast on the post it was cast on. These flags are often resolved as helpful when the post is edited, which ought really to suggest that the flag was wrongly raised, because a very low quality post by the flag's definition cannot be fixed by editing. It is often very annoying to me personally to finish improving a post only to find my efforts have downvoted it!
I almost never use the VLQ flag. If you want to use it, be aware that it is for unsalvageable rubbish, and not questions that are only poorly worded, spelled or formatted, or lack details we can request. Instead of flagging as VLQ, in any such cases, I recommend seeing if you can take any of these actions:
