I am a developer - not UX    
We don't have money for a UX person right now so we are just trying to get better at UX    
And the product has come a long way   
These answer that assert the product is too complex if it needs step by step instructions are not fair - you don't know the product nor our users   
We have competitors that have multiple online tutorials with voice over   
Accepting the question as stated I came up with the following design for the three types of help  
 - Manual - not UI   
 - Inline UI specific help  
 - One tutorial  

The manual stands on it's own and has chapters. 

Inline the instructions just describe the the button like IncFam means Include Family. 
For when users enter syntax we also describe the syntax inline.  We keep these close to the user control.  Always use an expandar with a standard look.  

We place links to the specific chapter both in the instructions and UI with just a simple ? link.  Like a pull down with a certain type of data we don't need to instructions tell the use what a pull down is - the ? link just describes the data.

For the tutorial we also use ? links to the manual.  And it is split screen with tutorial on the top and manual chapter on the bottom.  The idea is to teach them to fish.