The Complete Build It Yourself Package includes hex loaders for Windows and Macs. This is a tiny program that will upload the supplied hex software files onto your Arduino board so you can run the program.
An Arduino usually has a bootloader on it. A bootloader stays on the board to manage software uploads. When using one of the hex loaders, you may or may not be loading or even overwriting the bootloader. That’s fine; it just takes up space unless you are trying to load something from the IDE. Then the board needs to have a bootloader. Fortunately, the IDE has an option to first load the bootloader.
Sometimes DigitalCarbSync hex programs are supplied with and without a bootloader. Either will usually work. Sometimes the supplied hex program is too big to load directly if it also includes the bootloader. Just use the other version.
Here is some useful information about the bootloader.