The base set -- whether it is RotR or S&S -- has an introductory adventure (Perils of the Lost Coast for RotR and Plunder & Peril for S&S). For this introductory adventure, you should just use the cards from the base set, as well as the cards from the Character Add-On deck, if you choose to add that.
When you begin the main adventure path, you add the cards from adventure deck 1 to the cards you are using. After you have played the deck 1 scenarios and you are ready to play adventure 2, you add the cards from adventure deck 2. And so on.
The adventure path card has instructions for removing basic and elite cards after you begin adventure 3.
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That's it. Don't underestimate just how many cards you will be banishing starting at Adventure 3. In the group I've been play with, the only Basic cards we're NOT getting rid of are Allies that grant additional explorations and Blessings. Pretty much everything else is getting banished as fast as we can.
We're banishing BASIC trait cards as we close locations in addition to ones we encounter during exploration. By the end of the Hook Mountain Massacre we had filled up the Character Expansion box with the banished cards.
So you just keep adding the cards? So when you hit adventure 6 you should have all the cards from packs 1-6 minus cards you have banished from play?
Yup, you keep adding cards, but starting in adventure 3 you will start removing some cards. Instead of being by the deck number (in the upper right corner) it is based on the traits (upper left of the picture part of the card). The rule for removing cards is found on the adventure path card:
After you begin The Hook Mountain Massacre, whenever you banish a bane with the Basic trait, remove it from the game; whenever you you banish a boon with the Basic trait, you may remove it from the game. After you begin Sins of the Saviors, do the same for cards with the Elite trait.
It only applies when you are banishing cards, which isn't exactly the same as putting cards back in the box. For example, when a scenario ends you put any cards still in the location decks back in the box, but you don't "banish" them. So they aren't subject to the adventure path's removal rule.
So to your organizational question, separate everything out by the number (or letter) in the upper right corner. If you have the adventure deck tuck boxes, you can put cards 1-6 in their appropriate boxes. Or you can use dividers like these to keep them separate, but in the insert. Then, when you start a new adventure, add all those cards into the insert sections. You won't need to sort them out again unless you decide to start over again.