Ensure that there is a single path down the hierarchy to each single entity that you need to specify or record data about.
Use Two Models
Have one purely Hierarchical Model (the detailed analysis). Have another model, the methodology model that defines the analysis definition principles for demonstrating the general methods to be used. You can also use this as the reference model.
Start the Rules and the detailed models at the same time (they can even be in the same file, but eventually you will want to split them). In the early stages you can concentrate on the rules, using the 'detailed' model as an estimator, test bed and demonstration. As the rules become sufficiently detailed you can concentrate on the detailed model.
Rules models have a first page Table of Contents that is linked to the other pages by 'Jump Links'
Detailed models have a first page that contains objects that are linked to the other pages by 'Parent Links'
The first page is the Root. Only objects that are descended from objects on the first pages are included in the Instance tables. So at it is essential that page 1 is the top of the hierarchy.
Do not have unnecessary levels. For example a page one that has one object called Procedural Model and one called Physical model. You can easily have a number of each type of object on page one.
Use Class and data build frequently, from day one. Do not worry about redoing it later.
Only start populating the Class Generic and Instance tables when you have firm information. Once you have, you can still regenerate the tables, but it is slower.
See also S88 Modelling Guidelines