Are you doing a newspaper for print, or an online publication?
Right now I am doing the print version, but I will eventually be exporting a PDF version for online. Will those have to be separate InDesign files? Because I notice that the first and last page will have to be on the same landscape page for printing, but the online version will obviously be exported as separate pages. Any advice would be great. Thanks.
The size of your layout for print is going to be determined by how you print. It doesn't matter what size Onion prints on a large Web (roll-fed) press if youare printing a limited run on your office copier or at a local job printer. What size sheets does your printer handle? That's the information you need before you start.
There's no point in designing a broadsheet if the press handles tabloid (and probably vice versa).
As far as submitting the file for printing to a commercial printer, once you've figured out your dimensions and margins (in consultation with the printer), you will do the layout as a facing pages document set up to one half of the spread size so each page is independent. DO NOT ATTEMPT TO CREATE SPREADS AS A SINGLE PAGE IN ID. You will then export a PDF as single pages for the printer to impose and print. The odds are pretty good that you can use the same PDF for online distribution, but you may find you want to export a second version using higher image compression, and possibly RGB color space, to reduce the file size for faster download. You may eventually also decide that the online version is better as a real web page than as a PDF, but I can't help you there becasue I don't do that kind of work.
That layout as single pages should be in reading order, just as you expect the readers to see it when they open the paper.