Jim, It's probably one area that does unfortunately require a bit of familiarity with the programme methodology.
Start and finish counts are either marked counts or calculated counts. Split counts are always calculated from the displayed start count. The start count can be logged(marked) or calculated backwards from the finish point.
Basically when you specify a new course with the 'reset course' option from page two you will get a default start-to-finish layout with the start counter set to 00000. When you then specify the finish-to-start configuration (by pressing the S icon and seeing the reverse arrow from F to S) the start value will remain at the default 00000 and the finish value will remain as calculated (defaulted from the 'nominal' course length) UNTIL the actual finish count is marked whereupon it has the real value to back-calculate the actual required start count. The amber tags on page two should turn green when all the required information is present. Also on the full list on page four, selecting the finish point should show the status of the finish count - if it shows 'unmarked' then it is a calculated count rather than an actual count and it's awaiting entry of the real count.
If you are logging points as you do the measurement (ie from page three) then when you come to log the start point at the start of the ride (using the add button top right of page three) you will be presented with the option to log it as the 'nominal start' point whereupon an estimated finish point will be calculated along with the split point values you can expect. These will be updated at the ride's end when you get to enter and mark the real finish point. Again amber icons reveal assumed information that requires a final real input to complete the calculation.
I should add that this assumes that you are riding in the start to finish direction - hopefully I'll get the reverse direction ride algorithms for a future update as at the moment it will not count upwards from finish to start should you be doing a backwards ride. The presentation will always be listed with the start at the bottom and the finish at the top regardless - this is just having a convention of 'points ahead' being 'up' and 'points behind' being 'down'.
But would be easy to change if there is a demand!
Hope this helps.
By the way, if all else fails and the logging process gets into a complete tangle just press 'reset measurement' from the page two option, select the configuration again and enter the required counts into page four. Logged points are not deleted in this process - that only happens with the big red 'delete reference points' option.