They are the 2 formats that *nix systems use to store user mail.
If your MTA is /bin/sendmail, your mail is stored by default in /var/spool/mail/masterc in the ubiquitous mailbox format. When Dan J Bernstein
(aka djb ) got tired of the security vulnerabilities that constantly battered the sendmail daemon, he wrote an entirely new MTA called qmail. Since he wasnt too happy with the reliability of NFS over which /var/spool is usually mounted, he designed a new Maildir format to go with Qmail. More info on the advantages of maildir can be found here
But since Kmail looks like an MUA, it has to live with your existing storage format since all it is is a user interface to the mail storage area that is predefined by your MTA/MDA. If your daemon isnt Qmail, you should probably choose mbox.