There are three primary sources of 'how-to' help for PathFinder (as of this writing, a User Manual is not one of them :-). The first is the 'Protocols, info and help' menu which contains text walk-throughs and how-tos (with clickable links that highlight needed tools).
PathFinder Protocols menu

The second is the built-in 'Show me' tutorials, where the computer takes over the screen to demonstrate some of the essential techniques. Since the computer will be messing with stored strains, this is available only in UN-logged in states (it returns all the strains as they were before the tutorial, but why risk it?).
PathFinder Show Me menu

Lastly, there are three movies linked here, which were made using an older, uglier version of the program, but the functionality is largely unchanged. These are somewhat redundant with those above:

Movie 1: Basic operations (Plating strains; pouring plates, replica plating

Movie 2: Dissecting tetrads

Movie 3: Performing Temperature shift experiments

My apologies for the voice talent; with my budget, it's hard to get good help :-)