What I have set up now is that I can use Smart Login to execute the main bat logon script (seeing as Smart Login tends to only like BAT scripts) then using the bat script I have got it so that it executes our main logon script which is done using Scriptstart (Because I cant be bothered writing my own script. Seems to be working well now :D
Little late but ... Depending on the program your running via the batch you may have a dos shell window for the time you have the launched application open/running. So, you might also want to look into scheduled tasks to. You can set a program to be run at all sorts of times or events.