@Edison - yeah, I should've been more careful with regard to the order of the words - "paternal or maternal matches get matched to the Y or X [N.B. the order!] chromosome respectively." Good point. Luckily, dnapainter will match them appropriately if you select "Paternal" or "Maternal" relationship (rather than Unknown) for the match set.
@Thersa - determining whether a match on a chromosome pair is on the X or Y chromosome - there are a couple ways:
1. If you know the match is definitely on either the paternal side or the maternal side (from other information such as a family tree that you trust), then you can assign that match to the X (maternal side) or Y (paternal side) chromosome. Further, you can assign any other match with that person to the X or Y chromosome on the matched chromosome pair.
2. If you have already have another match (call it Match 1) on that chromosome pair which you have determined is on the X or Y chromosome, AND the new match (call it Match 2) overlaps the same region on the same chromosome pair, AND you check on gedcompare.com that the DNA kits for Match 1 and Match 2 are matches for each other, then Match 2 is on the same chromosome (X or Y) on any of your chromosome pairs.
Ex 1: You have a match with a cousin you know is on your father's side. You can assign all the matches with your cousin to the Y chromosome on any chromosome pair that gedcompare provides.
Ex 2: You have a match with an unknown person, and that match overlaps the same region (segment) with your (paternal) cousin. Then compare the unknown with your cousin on gedcompare. If they match, then you can assign any match with unknown to the Y chromosome on any chromosome pair.
In words, if unknown-someone matches you on chromosome 9 on a segment (say) from 9000-10000, AND your (paternal) cousin matches you on chromosome 9 from 9500-11000, AND your cousin and the unknown-person are a match, the unknown-someone is on the same side of your family as your cousin, and any of the chromosome pair matches with unknown-someone are on the Y chromosome.