You can put the name in brackets I think and Plex will ignore it. Since you’re using not quite right naming (see other thread) you sometimes have to fiddle to keep the “not quite right naming” but still be the way you like it to be … sometimes.
So in this case you should be able to get away with:
/Season 3 [name of season]
You might get away with:
/Season Name Season 03
If not, then naming the files S3E01 should work while leaving the folder name as is too - but that’s not what you’d prefer.
Sometimes we just have to conform to the parameters of the software even if it doesn’t match our preferences. 
Edit: I’d also suggest considering your fansub sources. Groups that use more standard naming conventions these days make this a lot easier too.
