So, I want to say that I have done the recommended suggestions that have been relayed to me here. I want to say thank you to everyone. It seems that it is working…
Stargate Atlantis > Season 1 > STARGATE_ATLANTIS - s1e3 - Hide-And-Seek
This seems to be working and I am doing this one at at time. I know time consuming but it is working. 
I will keep you up to date on my progress.
@Wolfclan1000, that’s awesome, however, do s01e03
This will keep it organized in the folder as well, otherwise you’ll get s1e1 and then s1e10 s1e11 etc. Plus it’s the proper naming convention, using 01 02 03 for season folder is also recommended
I have done the naming convention that you recommended and everything is working perfectly right now. I have used s01e01 and it is working like a charm. Thank you all for your help in this matter.
Going one episode at a time but I guarantee that I will not forget this.
Don’t forget there is Filebot
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