There really isn't a step-by-step to run the application, because it should run the same as on Windows.
If the application needs to run under a specific version of Windows, you can run 'wincfg', and set that (among other things).
Your Windows environment is in the directory '~/.wine/'. There are several applications installed in the Applications->System Tools menu (like winecfg) to help make using the WINE environment easier.
If you want to manually run a Windows program after installation, you can use a command of the format:
wine ~/.wine/drive_c/Program\ Files/SomeProgram/Some.exe
There's more information at the
WINE web site, and at this
user Wiki. If you have a specific question, you can post a thread in this forum.