Hi,
It depends on what thought you are trying to convey.
If you're trying to say that you've fully understood the message/email then just say so. i.e. 'OK, fully understood', or similar.
If you've read the message and haven't a clue what it means then say, 'Noted and not understood', or whatever is appropriate.
Which is why the original is not very useful since 'well' is open to interpretation.
Rgds