In Vixen 3.5 much of the Mark Manager functionality has been shifted to different locations or deprecated and removed.
Mark collections are now entirely managed in the Mark Collection docker. You can add/remove them, adjust their color, set their appearance and their type from the Mark Collection docker. You can import them from various different formats including Papagayo and xTiming which are both new in 3.5. They also can be exported in Vixen format.
Tapping can be accomplished by having a Mark Collection defined in the Mark Collection docker. Then with the collection you want to used marked as active, you can hold the Shift key and then hit space where you want marks to be places while the sequence is playing. Once the marks are added, you can later adjust their positioning within the timeline.
Pre Vixen 3.5
This section is still functional, however most of the functionality can be achieved more effectively with the new beat and bar detection features new to version 3.2.
Watch the above video for a short tutorial on how to create beat marks in Audacity and import them into Vixen 3.
As of the release of Vixen 3.1, the Mark Manger now has the ability to Export beat mark collections, in Audacity or Vixen 3 format. These exported collections can be imported into your other versions of a sequence, or shared with other Vixen 3 users.
Audacity can create a label track that includes the beats (and other things) in a song. Vixen has the capability to import these labels.
Audacity can use various plugins to analyze music and has basic beat detection built in. If you want more advanced beat detection, you can download other plugins for use with Audacity. I used the Vamp Plugins with some success (see video above). You can download them here: http://www.vamp-plugins.org/ .