It's not hard. Here's a quick and simple HOWTO with minimal explanations, for a TS source.
1) Make sure you locate and get SCXvid.dll and put it into the same directory as Yatta/YMC. This is a special version of xvid which helps the encoder by locating scenechanges and cutting the video up into sections. You MUST partition the video into sections if you want to use pattern guidance, and SCXvid does that for you.
2) In the YMC step, tick Cutter (to cut out unwanted ads), Telecide, SCXvid and Decimate. Run YMC with this. Once you open up the pregenerated .yap file, you'll see that YATTA will already have the video sectioned.
3) For VFR sources, make sure to enable all "Use c", "Use cccnn", "Use ccnnn" options for Pattern Guidance. For non-VFR sources, it's better to disable "Use c". (Access via Right-Click on the main window and selecting "Pattern Guidance")
4) Do "Pattern Guidance --> Pattern Guidance". Now, Yatta tries to determine the best patterns for the many sections there are. Here's the general idea: Almost all VFR parts will be all-c matches. So, after Pattern Guidance we'll have YATTA interpret all all-c sections as NoDecimate sections.
5) Now there's a small problem: Pattern guidance puts hard decimation markers on all relevant frames for recognized patterns. BUT to place a NoDecimate marker, you need to have a full cycle (5 frames) without hard decimation markers around. To ensure that the next step 6) doesn't fail due to that, we are lazy and just tell YATTA to delete _all_ hard decimation markers for now: (Right-Click on the Main Window --> Recalculate Matches --> Clear Decimated)
6) Now let YATTA convert all-c sections to NoDecimate: (Right-Click on the Main Window --> Recalculate Matches --> C Matches to VFR). If you now click on Tools and select "Ranges", you'll see the right table filled with NoDecimate entries.
7) However, we WANT YATTA to place hard decimation markers for the 23.976 parts. Therefore, we redo the Pattern Guidance step. It will automatically skip over NoDecimate sections now
8) We're almost done. Always do "Recalculate Matches --> Select lowest VMetric at Section Bounds" with Threshold 40 to make sure that there are no combs at the section bounds (which can be the result of Pattern Guidance, so DON'T FORGET!)
Well, that's essentially it. Do your normal YATTA magic with cropping, resizing, filtering and whatnot. When you let YATTA generate the override files, it will barf out all you need - the Avisynth file to encode the video to VFRAC, and a v1 timecode file for later muxing.
Done.