Pawel
In v1.4.2 of the PC version of File Flipper, if you go to Settings and select Coordinate System Library, you can hit the + key next to the Coordinate System Database and browse to find the version of the CSD file that you want it to use (that may contain your custom coordinate system. Then when you are creating Designs, and you select that you want to use GPS, and then select Coordinate System Library - it will now show the contents of the selected CSD file not the default one.
The online version of file flipper is much simpler and doesnt have the ability to use the Coordinate System Library, and Works Manager is basically the same - they both expect you to have a Site Calibration file - which you can create from SCS900 / Siteworks / Access or you can use Trimble Business Center to create.
I hope that this answers the question
Alan