Yes, as stated, I do have a few pointers. 

And I always LOVE to give suggestions that's "better than nothing"....

Now, don't get too frustrated here when (1) your post is sliced and diced and every typo, misuse of word, or contradiction-in-appearance (because you're dealing in different contexts with points that should be understood / deciphered by others) is analyzed and dissected to the kingdom come; or (2) your issues are taken off on a tangent with sub issues and possible sub-sub-issues are further analyzed and sliced and diced.

Sometimes, you'd see someone asked a simple question, and the discussions got more and more convoluted and more and more off the tangent from what the Asker needed.  (That would be when @Just-Lisa-Now- say she'd out while the others are getting more and more charged up.  But that'd be a different story.)   

In any case, I'm always glad to have such enthusiasm here.  Had we been medical doctors instead, patients would come in with plantar fasciitis and walk out with a kidney transplant...

Back to filing CA F568 for SMLLC of which the sole member is a pass-through entity.  I wouldnt say these are solutions, but for what it's worth...

1.  Lacerte (likely PS) supports efile for SMLLC in individual module ONLY.  Ideally, in your case, SMLLC (LLC A) would be efiled in the PS module under LLC B's PS (F1065) filing.  Sorry, NOT available in Lacerte.

2.  Consider this approach:

a.  Prepare LLC A's 568 filing as part of Partner Y's 1040.  (One of the @Just-Lisa-Now-'s earlier response seemed to indicate SMLLC efiling is available for 1040 in PS.)

b.  Manually enter the info for "Total income from Form 568" for Sch IW.  Because the income for LLC A was reported under LLC B and NOT Y's 1040, you would not be able to pull the total income info directly from Y's data. 

c.  CA is concerned about Total income because that's used to determine the LLC fees.

d.  Update the payment info.

e.  Enter the "Sole Owner" info to show LLC B.  The TIN and FEIN have to be changed and not Y's info.  Review the info carefully.  Because the info is off Y's file, you need to make sure all info is correct and the Sole Owner reflects LLC B.  (Lacerte has a section under "Sole Owner" for this)

f.  Question Q can't be overwritten.  Lacerte checks the NO box and can't be changed to Yes.  I attach a NOTE to state that due to software limitation, it was checked No, but the answer is Yes. 

g.  In the above software limitation note I also disclose the Sole owner is a Pass-thru entity and not individual (the owner entity info - printed above the signature line - can't be changed in Lacerte).

That was how I approached it.  So far FTB has not yelled at any of my clients.

One thing important: The due date for F568 for SMLLC owned by a pass-thru entity is generally 3/15 and NOT 4/15.  Mine are all write-up or compilation clients of mine.   As soon as Dec financials are done, I'd file them and do NOT wait for the 1065 or 1120S, let alone 1040.

Hope the above could be the "solution" you're looking for.  If not, add two words.  Change this to "not much better than nothing.'