The numbering systems are separate for each kind of resource, and are automatically separated by mod too - that is, ufopaedia image 301 for mod #1 is kept separate from ufopaedia image 301 for mod #2, and both are separate from handob image 301 for either mod. I think this is done by adding 1000 under the hood for each additional mod, so you can number up to 999 without any potential overlap issues. Just be aware that some types of resources take more than just one number, like a set of handobs for an item is one image split into 8 for each unit facing. Also remember that the vanilla xcom resources take up some of the numbers too!
Ruleset order does matter for how items / entries are ordered in the game, with mods coming after vanilla content, in the order they're loaded (ie, the order in the options), except when listOrder is used in the ruleset, and then it's numerically by listOrder. You can use either method to organize your items or articles, I just wouldn't suggest mixing them.