All VSL libraries (and every other library I have come across) are non transposed, so all transposition is done within the scoring software. Sibelius and Cubase for example both do this (and I'm sure everything does as well).
So play everything into the scoring software non transposed, and use the scoring software to transpose the view (it does not affect the performance). If you are reading a transposed score, then transpose your MIDI keyboard by 3 semitones to cancel the written transposition.
The only issue I can see using a Bb Clarinet instead of one in A, is that the A clarinet goes one semitone lower, so try not to use the bottom Db.
Although there may be an argument that an A clarinet has a different tone, but that's another issue all together.....