Basically, each class has two sets of skills, general and primary. So, choosing S/R, while Scout is primary and rogue secondary, you have access to both sets of scout skills and rogue general skills. When you swap classes to R/S, both sets of rogue skills available and scout general. Keep in mind once both are level 20, you can pick up a 3rd class, however you can only run as 2 of the 3, in any combo you wish. Each class earns their own exp/tp and debt, but only when they are the primary class. You also have 3 equipment slots for when each class is primary.
How you spend your tp is up to you. At various levels you get elite skills for specific combos. S/R has different elites than say S/W.
One last thing, when it says secondary can never outlevel primary, what it's really saying is that current secondary will never be higher level (therefore have access to higher level general skills) than your primary. So, if Scout is 10 and Rogue is 8, when you make Rogue primary, Scout will only give access to level 8 general skills. When Rogue levels to 9, the Scout General skills at level 9 will become available. Naturally, if you decide to keep going on rogue, when it becomes level 11, scout generals will still be level 10. You'll have to make scout primary and level it up.
I hope this helps somewhat. Head to the Scout or Rogue Class discussions for more specific info on the builds.
