Take a "Saga skill" and find which "RCR skills" contribute to it. For example, Perception in Saga uses the Spot, Search, and Sense Motive applications from RCR. So then:
"Saga skill" = Perception
"RCR skills" = Spot + Search + Sense Motive
Add up the RCR ranks that the character put into those particular skills. If the ranks add up to 5 or more, then make that character trained in that Saga skill (which adds +5 in Saga). If the ranks add up to 10 or more, then make that character focused in that Saga skill (which adds +10 in Saga).
Note: In Saga, you can train a number of skills at level 1 equal to your class + INT modifier. But to be focused in a skill, you need to take the Skill Focus feat.
Here's a couple more examples:
"Saga skill" = Deception
"RCR skills" = Bluff + Disguise + Forgery
"Saga skill" = Stealth
"RCR skills" = Hide + Move Silently + Sleight of Hand
As for Initiative, I would train it in Saga if the character is combat based or has a high DEX.