Hmmm, I seem to remember having an ongoing debate about the prestige (or lack thereof) of the WHC... if only I could remember the name of the guy I was debating with...
My feelings on the two belts since Easy E created the WHC for Triple H was for a long time very simple - whichever one was on RAW was regarded the premium belt and whichever one was on SmackDown was the secondary title.
Why? Pretty simple really, RAW has always had the far superior ratings and this has been reflected in who was allowed to hold the belt of the brand. Let me break it down from both belts existing (to keep it relatively brief, I haven't repeated Wrestlers names in each individual stint on the program in the spotlight)...
WHC
RAW
Triple H; HBK; Goldberg; Benoit; Orton; Batista (moved to SD)
SmackDown
Angle; Rey; Booker; Batista; Taker; Khali; Edge; Punk (moved to RAW)
RAW
Y2J; Batista; Cena; Edge (moved back to SD)
SmackDown
Hardy; Punk; Taker; Y2J; Swagger; Mysterio; Kane; Ziggler; Christian; Orton; Henry; Show; Bryan; Sheamus; Del Rio
WWe
SmackDown
Lesnar; Show; Angle; Guerrero; JBL; Cena (moved to RAW)
RAW
Edge, Cena, RVD (moved to ECW, quickly returned to RAW); Orton; Triple H (moved to SD)
SmackDown
Edge; Hardy; Triple H (moved to RAW)
RAW
Orton; Batista; Cena; Sheamus; Miz; Punk; Mysterio (kinda); Del Rio; Rock
What the above shows is that the RAW brand was always more prone to go with the established names whichever belt was 'Exclusive' to it at that time, the risks where always taken on the blue brand to see if that guy was worthy of the RAW belt. Despite the fact that the NWA / WCW link isn't meant to apply to the WHC, (because it is the physical old WCW Belt) it has been stated by those in the know that it was decided to be the SD (hence secondary) title back in 2009.
Now, while the WWe Title is the better regarded, very recent history indicates that even it only matters when it's around the waist of a headliner like Cena or the Rock. For the majority of CM Punk's
historic reign, the belt was considered secondary to whatever John Cena was doing and only really rose to prominence again when it got near time for the Rock to take it from him.
So, in answer to your question LSN, the WHC officially became the secondary belt when it returned to SmackDown on April 26th, 2009 as their
premier title.