so like my notebook rn is formated like [table of contents] 
[robot stuff following engineer and design process] [coding table of contents] [coding stuff]. we kinda did it this way cus we made our own library and we wanted to go super in depth on code and it was really hard to understand it it mixed in with the main robot stuff. is this fine?
As long as it gets the job done and it is readable its problably fine.
Separating building and coding is fine, especially if it uses confusing. However it is very important to have only one table of contents so a judge can see you also documented programming from just the first table of contents.
More than fine. Expressing as much as you can in an innovative way appeals to judges more than normal.