When you send a game to the card with the client software it puts the ROM in the root directory of the card. It makes a /Saver folder and puts the proper save file in it. You don't need to do anything manually as far as save files go. Sending a ROM creates a total of two files, the ROM itself and the .sav file in the /Saver folder.
I believe it auto trims the ROM, yes. Some games are considerably smaller than their original size. As far as I know there is no way to turn off this feature. Also as far as I know there is no negatives to this as I haven't ever had a game not work at all on the EZ4.
When you save in a game it saves temporarily to the battery of the card. The save is not actually written to the SD card until the next time you boot the EZ4. There is an option to allow you to skip the saving process, making the file as if you had not played your last gaming session. You can make it so that you cannot skip the saving process.
It is all done automatically, you don't need to do anything other than let the card and client do it's job.