The same question was also asked on the BB forums here; http://supportforums.blackberry.com/t5/Java-Development/Virtual-keyboard-is-hiding-the-part-of-the-edit-Field/td-p/2553879
The answer given involved creating a specialised manager which 'centered' a Field with in it, by overriding the sublayout for that Manager. Then the Fields to be centered where placed inside another standard Manager, which was added to the centering Manager. This meant the centering Manager had to deal with only one thing. the Final 'trick' was to define the MainScreen as non scrolling, which meant the centering Manager was given the height it could work with, and this height changed when the virtual keyboard was added, to the sublayout was called again and the centering Manager could adjust the position.
There is more on that Thread in the BB forums, including references to various KB articles and sample code. So please reference that Thread for more information.