GSD files are compressed log files. They're not necessary to keep on the card but you shouldn't delete them. For now, you can't do anything with them.
Everything in the GenesisLive folder is your file cache for Genesis Live. It needs to be on the card to preload Genesis Live with data.
The presence of a GenesisLive folder shouldn't affect what maps show up in the chart selection. If it does, you may want to perform a soft reset.