Hi Brandon,
Thanks for the question.

First, we'll map out the basic idea of what you will be able to do, then we'll give you the specifics (step-by-step). Connecting your guitar to the Motif XF can be done either direct (use the setting for Mic input and adjust gain) or you can plug your guitar into your amp and then you can Mic the amp. It depends on the sound you are going for.

The Motif XF will give you two Effects that you can route your guitar through (Insertion Effects) these will be recorded as audio. The two Effects called System (Reverb and Chorus) processor are not printed to the audio. What you are going to be doing is "Sampling" - Sampling is a type of audio recording but is different from regular audio recording.

Sampling has the following significant differences from normal or regular audio recording: samples are usually played from the beginning, by being triggered with a MIDI Note-On event that not only determines how loud it plays back, but also determines at what pitch it will playback.

You are not recording audio to a Track of the XF Sequencer. It's a MIDI Sequencer... all data on any of the tracks is always MIDI data. MIDI data that is assigned to playback audio, MIDI data that triggers an audio sample (What Yamaha did with the Motif-series was integrate a Sampler with a Sequencer. Your audio is will be a Sample, assigned to a Key of special Motif XF Sample Voice. This Voice has 128 Keys each Key can have a different recording. Each Sample is created and assigned a Note number, a MIDI event is inserted on the MIDI Track associated with this special Voice. The MIDI NOTE event will turn On the sample note, the Note's duration will allow the sample to continue to playback. This recording type is called "sample+note".

As you'll see you can automated both the Start and End of Sampling by setting punch In/Out points, these set the Note-On duration. The Integated Sampling Sequencer place the Note-On precisely at the punch in, creates a note duration to hold that note until the price point of punch out.
You will be able to use two Insertion Effects - including the new Guitar Effects

Setting up the A/D Input (general)
Microphone/Guitar to A/D Input

Setting up to Sample:
Sampling in Sequencer Mode

Exploring the Guitar Effects
Exploring the new Guitar Effects

Everything you told me as well as the links were very helpful. And now that I have tried all that stuff out I found a new problem that I'm sure you can help with. I am able to set up my audio-in sound settings, record to the pattern track I desire with sample+note, and even got into editing different things with the resulting track. I created a pattern I really liked with 3 guitar tracks which I found out the hard way is wiped out when powered off! I learned about having to store to the flash drives in order to keep your recorded samples intact. I am having a bit of trouble getting acquainted with storing my waveforms the proper way. Since you know the way in which I am using these waveforms in patterns, can you guide me through storing my recorded tracks so that they are there in the pattern right as I left them with all effects and settings intact. Also it would be great to have a single track that plays multiple samples by using different keybanks rather than making an entire new waveform everytime (I hope I said that right).

You are making excellent progress... you said that perfectly.

Yes, samples are initially recorded to volatile RAM (Random Access Memory). In the XF, this means when you power down your samples will disappear, much like working in RAM on a computer, you must SAVE your data in order for it to be there next time you power on. This has been the nature of audio Sampling since it's inception back in the early 1980s.

When you Sample to the XF's Integrated Sampling Sequencer (ISS) you are actually creating a User Sample Voice. This Voice can house as many as 128 Stereo recordings ... for example, one per Key C-2 Thru G8. Each recording (sample) can be directed to a specific Key. The MIDI data (Note-On events) are documented to the Sequencer Track, each targeting a different Key of the same target User Sample Voice, as you overdub.

In the screenshot above, the User Sample Voice will be created in Part 16, the sample is targeting Key = C3.
If you were to proceed and record the Sample, a Note-On triggering C3 will be created documenting the 'in' and 'out' using note duration. This will be used to playback the sample.
You would setup to record your next sample to Key = C#3... you will be able to hear C3 playback as you add new audio to C#3, and so on, to D3 and D#3, etc. No need to change the Track just increment the target Key. In MIDI every track has 128 Notes, C-2 Thru G8... and each can be set to trigger a different stereo sample.

You must [STORE] your work... the User Sample Voice is automatically assigned to your Pattern Mixing setup, when you STORE the Pattern it gets stored ... but to insure it will be available the next time, before you power down, you must SAVE your data to either an ALL data or ALL PATTERN data file.

STORE - is the act of writing data to the Motif XF's internal memory.
SAVE - is the act of making a file that will allow you to restore data to the internal memory.

Only the Stored data will be Saved by the SAVE operation. So you need always to STORE changes you make - like adding a VOICE to a Pattern Mixing Part... then for long term storage you need to create a FILE... SAVE always creates a File and that file backs up and allows you to restore all of your work.

If you are working on a letter in a word processing program, you are working in your computer's RAM, you must create a file so you can restore it later. Here you also must create a file (to a USB stick) so you can restore your work at another time.

Sample data can be quite large and is volatile- disappears on power down - so SAVING data is required.