Instant Text and AutoCorrect
There is no conflict; they work well together. My advice, though, would be to import your acl file to create a glossary and see how you get on.
Apart from anything else, MS Word is notoriously unstable when it comes to AutoCorrect, and I know I'm not the only one who suddenly lost everything one day! If you have an IT glossary which you have become used to using, it's no big deal if that happens to your AC file.
Also, your abbreviations would be available in all programs (email, for instance) when linked to IT, not just in Word. Finally, you can always choose to import only the true expansions, leaving the typo corrections in AutoCorrect, which is what it was really designed for in the first place.
JMO, hope it helps,