A normal region is just a sequence of consecutive flash blocks (their addresses are fixed in a special table inside firmware parts: fw_all.bin, boot.bin and others). Also there could exist degenerate regions which are mapped to files and maybe entire CF cards. I don't know the whole story.
Regions are addressed by 1-byte region number. So valid region numbers are 0-255 or 0x00-0xFF.
Here are some most common region numbers:
0x05 - bootloader
0x0C - boot.bin
0x0E - fw_all.bin
0x2B - x-loader
Roughly speaking, RGN file is just a bunch of regions which could be transferred to a device by updater.exe or WebUpdater.exe over USB or Serial.
GCD file is a sequence of sections, each of them has a few additional attributes, like Type, HWID, Version, and a few other minor ones.
Type determines which region the section is mapped to. For example, section 0x0008 corresponds to region 0x0C, 0x02BD - 0x0E, and 0x5XY - 0xXY, and so on.
HWID determines the device which the section could be flashed to. It's possible to combine sections with several HWIDs in one GCD file and only the matching ones would be flashed.
Version is pretty obvious.
Commands from update.txt like rrgn,ergn,xrgn work with decimal region numbers. They are used for reading,erasing,writing regions respectively.
RGN_Tool is able to load/save GCD and RGN files and display the list of sections/regions inside them. In the leftmost column it displays the section number and in the rightmost column it displays the region number.
I hope this explains everything.