I think that you really need to read the Tooltip NT instructions before you get a ton of work involved in this. I'll try to give you a few hints that might help.
Yes, each book will need a mark.
Did you set the file type with Module Define Variables (i.e. Topic, Bible, etc.)?
Did you save the file as that file type before trying it in e-Sword?
Philippians 4:6-7 (KJV)
6 Be careful for nothing; but in every thing by prayer and supplication with thanksgiving let your requests be made known unto God. 7 And the peace of God, which passeth all understanding, shall keep your hearts and minds through Christ Jesus.