App Studio applies an algorithm to determine the most likely ruleset into where a new or changed rule will be saved. Inputs to the algorithm include the current layer of your Branch development preferences (if you are using Branch development), the Applies To Class determined for the rule, and whether this is a modification to an existing rule or a brand new rule.
By limiting the scope of a Branch to a single feature, this simplifies (using Dev Studio's Branch landing page) the task of reviewing the rules that comprise the feature, including the Class and Ruleset decisions App Studio has made. When App Studio has not read your mind and chosen an undesirable Ruleset, the Branch Review is the ideal time to override this by re-saving the affected rules into the Ruleset you intend, and re-running your test cases to assure they continue to pass.
As a LSA, where your design requires intricate positioning of rules in specific Rulesets, implement placeholders for these rules in the required Rulesets using Dev Studio, and empower your delivery team to pick up the relevant versions from App Studio where possible. There are times of course where the developers of such features will need to work in Dev Studio to retain full control of the Rulesets new or changed rules are saved into.