Where do I put these Rules?

So, you are going to follow my advice and just start building, you hit 'new activity' and staring you in the face is the first unanswered questions: What class and what RuleSet? You didn't get very far. Now what? Here's the idea. Classes can be renamed and RuleSets can be merged. So:

Class strategy: what is the general type of class you are using Work-, Embed-, or Data-? Don't worry about pattern inheritance (aka named inheritance) for now. Just name it Embed-xxx and save the harder decision for later. Once you figure-out where the class should really live, go to Tools -> Rule Management -> Rename a Class and pick a new name (make sure you have backups first just in case).

RuleSet strategy: Moving rules from one RuleSet to another is a pain for large volumes. It is basically just a Save As + Delete. But, it is very easy to merge two RuleSets. So, make this work for you by creating a new RuleSet to hold your early rules on their own. I like to name them Helper_xxx_Base to set them apart from more permanent RuleSets. After you decide which part of the puzzle they belong to, go to Tools -> Rule Management -> Merge RuleSets. This makes pushing a small RuleSet into a larger collection easier.

Taking these step will give you a simpler path to refactoring your work using Pega's automated tools to do the heavy lifting. It should give you the mental freedom to start working without needing to know exactly where you are going. Get started and keep going.