A Tricky question regarding when to bottle.

I made a noob mistake, I transferred to secondary before the Krausen was done Krausening. That is, prematurely. I have no idea what this means, and I can not find the answer in any book.
My inaugural batch sits in the "Secondary" fermenter. A brown layer of Krausen sits upon it. I don't know whether to wait the standard two weeks of secondary or pull it out after two weeks total. To clarify, a chart:

Friday: Brewed, placed in Primary
Saturday: Bubbles
Sunday: Bubbles
Monday:Bubbles
Tuesday: Bubbles
Wednesday: Overeager, transferred to secondary. Still thick krausen on top.
Thursday: New Krausen develops
Week One over.

Friday: Bubbles and Still a Krausen Layer
Satuday: Bubbles and Still a Krausen Layer
Sunday: Bubbles and Still a Krausen Layer
Monday: Today! Bubbles and Still a Krausen Layer

So do I treat it like a standard primary batch and bottle this Friday, which would be two weeks total in fermentation, or do I go two weeks from the date it was placed in secondary.

Your help, as always, is appreciated.

for sure if it's still fermenting and you bottle - you will have succeeded in creating bottle bombs.

at this point i would say let it continue it's fermentation cycle until it is visably or measurably over.

then allow to mellow an additional week or so then bottle

You can always do a tertiary ferment. Wait until the krausen has completely fallen, then rack again, wait another week or two, then bottle. You'll have nice clear beer.

I believe the main issue here is the clarity of your bottled beer. It should finish up fine in secondary, but you'll probably wind up with more trub than if you waited a little longer to rack it.

As Kephren said, do a tertiary if you're worried about clarity. Otherwise, let it finish out and bottle it up!