There are probably several ways to do this, but here's one I thought of. In the fly-out menu of the Pages panel, you will find Apply Master to Pages…, where you can specify a range of pages to apply your masters to. Supposing you had 200 pages set to A-Master, and you wanted to apply B-Master to all even pages, you would type 2,4,6,8 etc. up to 200, into the field, and you will be done.
To speed things up, you can use Excel to generate your numbers. Enter 2 into a cell, then 4 into the next lower cell. Select both cells, click in the lower right corner of the bottom cell and drag down. Excel will fill in numbers based on the pattern of the selection—in this case, even numbers. Copy those numbers into InDesign and use Find/Change to change paragraph returns ^p into commas (for just that story that contains the numbers). When it's done, you will have all even numbers from 2-200, which you can copy and paste into the Master Page panel we talked about before. I just tried it, and it took less than a minute.
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Just work with spreads, export normally and select single page layout in Acrobat.
Acrobat>Properties>Initial View>Page Layout.
Having read Haakenlid's response, I must admit I missed the point of your question. If all you want is a larger inside margin, you don't need to go to the trouble of applying alternating master pages. Within the margins and columns window, there is a place to set the inside margin separately from the outside, but maybe the lock tripped you up. With the lock engaged, all margins will be equal, so click the lock icon if you need. But if you need to alternate your master pages for some other reason, my method will work.
I'm not sure it's entirely clear from the previous posts at this point, so I'll say it directly.
In Document Setup check the box for Facing Pages. Set a larger inside margin if you need it. If you've already set up as non-facing pages you can change that. First go to Layout > Layout Adjustment... and turn it on, then go to Document Setup and enable facing pages, then select the Master page in the Pages Panel and select Master Page Options from the panel menu and change the page count to 2. Withthe master page selected, go to Layout > Margins and Columns... and fix the margins. This is complicated enough that if you haven't done any real work you'd be better off starting fresh with a new facing pages document.
Facing pages is only a display option that allows you to view and edit in readers' spreads for convenience, and to use a two-page master so that you can have different left and right pages without jumping through hoops when you add or remove pages. It has no effect on what gets exported to PDF when using the PDF (Print) option (in CS5 or 5.5) or in any version earlier than that unless you deliberately choose to export spreads (which you should not) by checking the box inthe export options. PDF (Interactive), though is the default choice in CS5/5.5 and it does automatically export spreads as well as not give you a print quality PDF, so be careful and choose the correct option. Your PDF will be exported as single pages, as the publisher wants.
Thank you all for your replies. The answer seems pretty obvious now that I think about it.
Very elegant solution. Thank you!
Perfect for when you need to make changes to a document that is already laid out. In my case, a perfect bound notebook (bound at the top) where there is consecutive page numbering at the bootom of each page. A .5 inch margin was needed below the page number of the 'upper page' and a .5 inch margin needed at the top of the 'lower' page. however the book had been laid out with .25" all around, and designed within those margins. The even pages being the 'top' page I had to adjust the bottom margin for that master page so that any text extending too close to the bindingh could be moved.