Workbench Reach Another Datafiles Directory (no replies)

Hi, firends.

I run into a datafile directory problem.

When I connect to server using cmd, I get datafiles in below directory, designated during installation process.
C:\Documents and Settings\All Users\Application Data\MySQL\MySQL Server 5.6\data

But if I use workbench, it get datafiles in the data folder under MySQL Server directory. The same happens usng navicat and Mysql front.
D:\Program Files\MySQL\MySql Server 5.6\data\(installation folder)

So I get two folders with different datafiles even with same localhost and user. This is not wanted. I tried to modify datadir in my.ini as the second one, but server cannot work then.

I'm confused about the different datafiles. Any comments?

Thanks you.
Wei