I'm doing the study (slowly!) I don't have a flow chart but the sequence would be:
Finish draft accounts.
Start a new Ct600 and click on trading profits.
From there you can add various sections the most likely being: Trading Income
on that section:Go to Data Input and: Enter turnover (manually)
Then do Adjustments To Trade (things like entertainment, depreciation etc)
Then do Cap allowance and hey presto you should get a tax computation.
Then its back to the accounts to make the adjustments for corp tax etc (based on the assumption you use Taxfiler to do the computation)
Then you have a draft of accts and ct600 for client approval.
Thats how it appears to work on the Taxfiler demo site
As far as I can tell Taxfiler won't populate the Ct600 because the figures used for the tax comp are not the same i.e depreciation in the accounts is nothing to do with Cap Allowances on the Ct600
Hope that helps a bit.