This is a tough one to solve easily. The original software (now in version 3.11) was developed over 10 years ago with features not found in the new software (VUMIE 2012), and vice versa. Basic Training Manual and Micro Lab Basics are lab manuals written for the feature set and appearance of the 3.11 software. They, by their very nature, don't match up well with the new software. That is why Micro Digital Media was written - to accompany the new software. MDM and VUMIE 2012 have left behind some orientation exercises that we felt no longer to be important, since the computer skills of average students have surpassed the need for training students to drag and drop or right click to reveal options.
In some ways, it is like trying to apply the content of a 2001 Toyota owner's manual to a 2012 Toyota...technology and features and placement of controls are not the same. But both will still get you from point A to point B.
That said, once you get past the actual appearance and orientation to the virtual lab, you should see little difference in the way 3.11 and VUMIE 2012 function. Creating unknowns, selecting media, aseptic transfers, incubation, addition of reagents, using the matrix to identify an unknown - all of those things are done in the same way in all versions of our software.
So work with your instructor to determine how to get past the orientation exercises in BTM and you should find the other exercises to parallel those done by users of 3.11.