I feel for you - I've been through a steep learning curve like this too - though mine is with Moneysoft Payroll Manager and NEST, so it's maybe not been quite as painful. I'm afriad I don't know how SAGE payroll works, so can't comment on how to set NEST up with SAGE - only NEST with Moneysoft.
From my experience, it could be that in order to have changed the pay period from 1st to 30th to 6th of one month to 5th of next, you will have had to change the 'GROUP' from monthly, to TAX monthly. When you change a group, it takes overnight for these to update on the NEST site, which is why they will have talked you through doing the calculations the way they did - probably using the Exceptions submission, rather than the normal method of Contribution Submissions.
Also, once the GROUP has updated, you have to ensure the WORKER is changed into that GROUP, and that that has updated (overnight!) So providing you revisit this in a day or two and make sure its 'prepared' for next month, it should go much more smoothly for you 'uploading' wise.
Don't forget to click on the 'PAY' button in NEST though - to make sure that you instruct NEST to actually take the Direct Debit, this doesn't action unless you hit that button!
The difference between pensionable pay and qualifying earnings is this:
Pensionable pay - all basic salary income from £0 - see a bit more on this here http://www.thepensionsregulator.gov.uk/docs/dg-4-appendix-f.pdf
I may be wrong - but I think you can exclude overtime and bonus from this calculation - but I don't have anyone on this scheme as yet, so haven't studied it yet
Qualifying earnings - this is linked to the NI earnings levels - so is all pay - including overtime, bonus etc, but doesn't start until £486 per month / £5,824 per annum
More here http://www.thepensionsregulator.gov.uk/automatic-enrolment-earnings-threshold.aspx
Hope this helps to clarify a bit more..........! The Pensions Regulator Site and the NEST site have loads of info on this - you really need to study it in detail if you're going to understand it better!