Q: hlp.sys is not found when I try to start pcitree.exe.
A: copy the file hlp.sys to the Windows directory (see userguide)
Q: is it possible to get the source code of PCItree?
A: No, I'm sorry.
Q: does PCItree run on a 64bit Windows system?
A: No, PCItree only runs on a 32bit system. It is on the todo list to add 64bit support to the driver but with low priority. Meanwhile you can try to use an XP emulator on Windows 7 Professional and run PCItree on it.
Q: how does PCItree access the config register?
A: PCItree uses Port-IO reads and writes to the addresses 0xcf8 and 0xcfc. By this the config registers can be accessed. See PCI spec v2.1 chapter 3.7.4.1. Configuration Mechanism #1.
To use Port-IO you can look at http://www.beyondlogic.org/porttalk/porttalk.htm or WinIO.