Here's another thread containing many ideas how to align MFT fence and Guide Rail to get square cuts.
Square MFT. My personal favorite is to use a large reference square to set the MFT fence square to the Guide Rail. I use an 18 inch precision carpenter's triangle from Woodpeckers. This same tool can also be used to lay a pencil line where you intend to cross cut and thus to confirm alignment of your planned cross cut
before it is made. In this photo, the precision triangle is the gold colored item which I am using to confirm that the DeWalt T-square accessory is ninety degrees to my Guide Rail.

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To get parallel strips that you will later cross cut into shorter lengths, there are also many ideas on FOG. I prefer use of stops or a story stick. Jerry Works manual on uses of a Festool MFS shows how to make and use such stops for accurate, repeatable parallel cuts. I made a much less expensive version.

To use these shop-made stops, first lay the Guide Rail on the sheet to be cut and rip a straight edge. Then make a pair of pencil marks at the desired strip cut width using a shop rule or tape measure. Then set the Guide Rail with its splinter strip on the pencil marks. Then set
both shop-made stops to the required width setting, with both stops being placed on the Guide Rail next to each other. Then relocate one of the preset stops adjacent to the other end of the Guide Rail, reset the Guide Rail, and make the rip cut. You can now rip as many pieces as you need using your preset stops and all will have parallel sides and be of identical width.
Note that many roofing or framing squares are not square. They may be close from the factory, but not precisely square. You can check any square to determine if it is truly square by using it to draw a pencil line that is presumably perpendicular to your reference (base) edge with the handle of the square extending to your left, then flipping the square 180 degrees so its handle is extending to your right and drawing another line on top of or very close to the first line you drew. If the lines are not coincident or parallel, your square is not square.
Dave R.