Upload File Program in Sharepoint and Timeout occur

Dear All,

I have written a program in sharepoint, in which will call a Web
Service of another Sharepoint portal server so that documents from
sharepoint portal server A can push document to Sharepoint portal
Server B whose domain is stood alone.

However, the program is unable to upload file over 2MB, when the file
size exceeds, timeout will occur! I have tried to make a change in the
web.config and machine.config of sharepoint portal B but I found that
the original setting should allow file transfer up tp 4 MB! Moreover, I
have looked into the Application Pool Setting of the portal B. But I
have no idea how to set the time out length in IIS 6.0?

Can anyone help me?
Is that I have to add some timeout configuration in the web service ?
What should I try then?

Thanks a lot