I don't have experience with the tool room series but I have quite a bit of experience with my Haas lathe. You have all ready answered your question. The machine doesn't know were each tool is unless you set an offset for each tool and call it up in the program. It should work just like my machine but instead of a turret being indexed you are manually changing tools. I would assume your programs look like this when going for a tool change:
G00 G28 (RAPID HOME)
M00 (PROGRAM STOP, CHANGE TOOL)
Txx (THIS WOULD BE THE TOOL YOU CHANGE TO. IE T01 OR T02)
If it looks similar to that, every tool your going to use in the program should be set up in the offset page.