If I root my Asus Transformer, will I still get and install the manufacture updates?
When you root your device you're gaining administrator access to it (root). Nothing more nothing less.

So, unless you install a third party ROM, you will continue to receive updates and be able to use the source code you download. One small issue, updates may unroot your phone if you install them.



Some useful reading on this subject:


What does “to root a phone” mean?
Are there any risks to rooting a device?