Two orange squares…hmmm,. I’m guessing that it’s a screenshot of the pattern sequence?
The pattern sequence is representing the order of patterns (the sequence) in your song, and the number refer to the pattern at that position. You can doubleclick to change the number, or use CTRL + left/right arrow keys to switch between patterns on the fly. If you don’t want this (repeating any patterns in a song), you can also right-click and choose “sort and delete unused patterns”
As for the highlight, it’s, well, a visual guide. It doesn’t do anything as such, but you can change the way it’s behaving in the lower panel -> Song settings.
It’s the feature “Highlight every xx blocks”, found in the Song Settings tab as danoise mentioned.
It’s quite a useful feature, really. If you typically arrange sections of your song into groups of 4 patterns, for example, then you can set the highlight to change from light to dark every 4 patterns, and that just gives you a nice little visual clue about your song structure.