Big World Setup Questions

Last time I used BWS I installed the EET Mod along with a few others and the result was a few dialogue bugs where Chapter 1 dialogue was replaced with dialogue for much later in the game. I didn't make it past Chapter 2-3 before I ended up becoming too busy to play the character and erasing my game so I don't know if it would keep popping up or not but it was a major issue.

How can I use BWS to set up my mods without using EET? As great as it was I don't really feel as if it is a neccesary mod.

If I can't do this how do I avoid a major bug like this? Are there mods that don't work in conjunction with EET?

Please help.