I am slightly confused as to the question.
To rack, simply siphon your beer from your primary to your secondary with minimal splashing to avoid oxidation.
To do this, remove any stopper from both carboys. If you have a racking cane or auto siphon, perfect: make sure they sit beautifully above the trub. If not, siphon to the secondary keeping the hose in the primary above the trub like we were talking about earlier in the thread.
I have seen people siphon through the stoppers, which is what I think you are mentioning, but I do not like it nor have need for it. It has the advantage of holding the siphon hose at a specific place, but I found it a pain to manage. If it works for you, go for it!
Whatever route you take, make sure you do two things:
1. Minimize amount of trub you take with you. This is, of course, one of the reasons we are even using a secondary in the first place. Be patient, there is no need to rush. Prepare before you begin siphoning, because you ideally want to only start that siphon once.
2. Minimize oxidation. You got this far with the beer, and particularly since we are trying to REFINE the beer, don't chance hurting it. Avoid splashing the beer directly down into the secondary, and try an avoid starting the siphon multiple times.
And of course, avoid any contamination! I feel like a parent saying this, but sanitize!
Question us more if need be, I for one don't mind replying. And if you are all set, let us know how it all turns out!
Cheers