Hi Gernby,
Regarding the UltiMate GPS App v3.0.0, it does not include any
new firmware. Original UltiMate GPS production units were shipped with firmware 1.0.4 so we always include the latest firmware in any app updates so that users who have never upgraded from firmware 1.0.4 can easily do so.
So if you are already at firmware 1.0.6 (which sounds like you are already), the app won't let you upgrade firmware again. It will tell you your firmware is already up to date.
Just as a side note, the firmware upgrader in the app was designed to be foolproof

. Even if the user would unplug the accessory or quit the app during a firmware upgrade, nothing will happen to the accessory and you would just restart the app and try again.
With respect to v3.0.0 of the UltiMate GPS App, it includes AGPS data upload. This has nothing to do with the firmware though (although the upload process will look similar from a user interface point of view). What the "Upload to Accessory" button does is upload two weeks of AGPS data (assisted GPS data) to the accessory. AGPS data contains satellite orbit information to be used by the GPS engine in the accessory to achieve faster locks.
Give it a shot and upload AGPS data with the new app and you will notice that you have faster lock times (in the mornings) when you start first using the accessory again after it has been of for a large amount of hours or a day for example.
From my own experience, I usually use the accessory in the early morning while driving, then normally don't use the accessory again till the next morning. With AGPS data uploaded, I can see a much faster lock than without AGPS data uploaded. Typically it improves from about 30sec to 15secs.
There is a "Clear Accessory" button in the new version of the app as well, so you can put this to the test yourself. Just try it out one morning without AGPS data (just clear the AGPS data with the "Clear Accessory" button) and then the next day, try it with AGPS data uploaded. I am sure you will notice what I am trying to describe here
But note that you won't see any difference if the accessory has already gotten a lock on a certain day and then immediately you try again as then the accessory will be going from a hot start (which is usually only a few seconds) compared to a warm start. In order to see the faster lock times, at least some hours need to have passed between your experiments (so that satellites will have moved significantly in orbit in that period).
Hope the above explanation is clear. If not, feel free to ask any further questions.
Roger from Emprum