For your application, as long as you meet the required current limits - I do not think you need to worry.
Transformer output voltage will vary, it will be a bit higher than rated when open, and lower than rated when you draw current from it. So it has two output windings, at 18VAC @ 3.6A max. Providing you draw <3.6A from either winding (independantly, or at the same time) I'm sure ti'll be fine.
Also remember, if you're using each secondary output winding for a seperate supply, ALL regulation circuitry uses up at least some current. So even if you are not using one of the two supplies, it will still draw *some* current from the transformer for the regulation circuit - it will have at least some form of load, albeit very small.
As for the primary (mains) side, I believe you must use either series or parallel for the voltage you wish to run it off, this is so it can deliver its rated 130VA. If you only connect one primary winding to 115VAC, you could only draw half the power form the secondary side.
I'm not sure where you got that 'quote' from, the datasheet doesn't mention it - although it does specify that the windings are 'not intended to be used seperately'. To me that just means the voltage regulation spec will be out, giving you a higher or lower output voltage should you just use one winding.
I don't see anything special aobut that transformer that requires different design from any other mains transformer, just abide by the ratings and you'll be fine