Hopefully this is the short answer you need... yes, you should be able to cut and paste the contents of your SD card onto your HDD in fat32 format. Forwarder files will (generally) check SD:/apps, then it will check USB:/apps after. You can load apps from the HDD in homebrew channel the same as you would from an SD card (although you may need to hit 1 and select "Hard Drive" as opposed to SD, but probably not).
If all of your backup needs are being met from USB, then you can get rid of Neogamma if you really feel as though you will not need it, just keep in mind that you (as of this posting) cannot load Gamecube backups from USB, and can only use disc, and Neogamma is the better way to do that.
And on a personal note, fat32 is by and far the way to go (even though i use fat32 and NTFS, personal choice, multimedia storage) so you are making the right choice. Keep following guides on this site, and you should be fine.