So when I try to add new trunking system manually I click on save changes but it doesn't save them.
Not sure where you see save changes that you are clicking on, in EZ Scan information added or changed is automatically saved when you exit out, and it doesn't go to the scanner until you click on copy configuration to scanner memory card.
On the Trunked Systems tab click new, add system including the correct type, go to the bottom and add sites (you only need the control channel and alts), talkgroups and Radio IDs if you want them (at least just add wildcards in TGs and RIDs). Then go to the Scanner/SD Card tab at the top and copy to scanner memory card. Card can be in computer for faster and more reliable transfers.
But why are you manually adding systems rather than using the database?