Pairing up is generally initiated by DSB and homologous chromosome directed repair.

During Prophase homologous chromosomes pair up. A large influence of this is DSB repair via homologous chromosomes (induced via mol. mechanisms). Many DSB repairs induce juxtaposition of chromosomes allowing formation of a synaptonemal complex, which is zip like and holds chromosomes together. Later they are only held together via crossover points.

The Male sex chromosomes cant really pair up during prophase, they are silenced transcriptionally via chromatin modification and kept to a special domain called the sex body. HOWEVER, they do have some small regions of homology which allow recombination after DSB which allows them to pair up through repair. These are known as psuedoautosomal regions - a small number/area can be recombined in sex cells. Thus you get a pairing.

Chromosomes dont wan't to join up at centromeres because they ultimately join via crossover points in Meiosis, and breaking a centromere would mean improper disjunction.