Save your repaint as an image file with a helpful name (e.g. if I was making a Stagecoach repaint of the C400R I'd save it as Stagecoach_Exterior.png or similar). You'll need to place it in the repaints folder of the bus you're repainting, this will be inside the "texture" folder, likely something with "Repaints" or words to that effect in the name (the C400R uses "Livery_R"). You will then need to create a CTI file (files ending with *.cti). You'll likely see at least one already in the folder, so you can make a copy of it and edit that copy for your own repaint. Omsi will see any CTI files in that folder (but not any sub-folders), and each file can have more than one defined repaint in it (it's best to create your own instead of editing an existing one as it's easier to distribute that way). Inside the CTI file you'll find a series of entries that look like this, but with slightly different values:
The top line is the name of your repaint. Your repaint may have several of these [item] entries and they all have to have the exact same name otherwise they'll be considered as different repaints. This name is what is shown in the list of repaints when selecting a bus. The next line indicates to Omsi which texture of the bus you're replacing. The exact entry you need to put here will vary depending on which bus you're using (I set the C400R to use helpful ones, like "Exterior"), but you'll likely have to deduce which does what by seeing which value is associated with which image on existing repaints. The final line is the repaint file you saved earlier, it's what Omsi will replace the default texture on the bus with. This line can be a path in addition to a file, so you can place your images in a sub-folder if you so wish. Bear in mind that if this is incorrect in some way, the bus will have a blank white texture there instead.