Read the documentation! Most questions are answered by
http://pobox.com/~djb/qmail/pictures.html) which show how qmail
handles various types of messages; /var/qmail/doc; and /var/qmail/man/cat*. Your system includes a wide variety of monitoring tools to show you what qmail is doing:
/var/qmail/doc/TEST.*; 
instcheck (in the qmail install directory), which looks for
installation problems; 
qmail-showctl, which explains your current configuration; 
dot-forward -n (if you have installed dot-forward), which lets
you see how a .forward file will be interpreted; 
fastforward -n (if you have installed fastforward), which lets
you see how a forwarding table will be interpreted; 
ps, which lets you see what processes are running; 
recordio (if you have installed ucspi-tcp) and tcpdump,
which let you see what data is flowing over a TCP connection; and 
trace or truss or strace or
ktrace, which lets you see exactly how a program is interacting with the
system. If all else fails, you could try asking for help on the qmail mailing list
(
http://pobox.com/~djb/lists.html#qmail.)  Your message should give
complete answers to the following three questions: 
For checkpassword and other POP password checkers you should instead try
the password mailing list (
http://pobox.com/~djb/lists.html#password.) For serialmail
and other part-time-dialup questions you should instead try the serialmail
mailing list (
http://pobox.com/~djb/lists.html#serialmail.) 
Yes. See 
http://www.qmail.org. 
pobox.com/~djb/im.html explains the Internet mail infrastructure.  
http://pobox.com/~djb/smtp.html explains the Simple Mail Transfer
Protocol.  
http://pobox.com/~djb/immhf.html explains the Internet mail
message header format.