To learn to program the radio, fist start by getting familiar with it. the book is a very good place to start. There are a few things you will set for your repeaters. Each area of the country has a PL tone to keep the repeaters from interacting. So whatever that PL tone is, is something you set in the radio menu of settings.
The general idea is put the radio in VFO mode and dial in the frequency for the repeater output. Then make sure the offset is correct, then the PL tone is correct, and set to whatever the repeater calls for. The tones are accessed by one of the front buttons, and the button cycles through several possibilities.
The most likely tone control is Enc, short for Encode. That means that your radio will only send tone, not need to receive it There are a few choices, stop when the display shows the proper tone setting. the frequency of the tone is set in the menu. Once you have a frequency, offset, and tone correct, test it by accessing the repeater. If you don't activate the repeater, you have something that is not right. Once you have it all right, you want to save it to a memory location. the book describes how to save to memory locations.
I can't stress enough how much you show try to join your local Ham Club, and make some Ham friends. My Ham Friends have been lifetime friends, I've know them for longer than I can remember. Hams all have one thing in common, they love to help others. You will learn much from other hams. Then there is the Internet, Google can help you learn anything, including ham radio. Good luck, and don't worry about asking questions. I have the FT8800, and it programs just like the 8900, and some others, including the TYT-9800, which is a Yaesu knock off in every way but quality.