When you start to work with a new tool, it's always worth taking the time to learn to use it as itself. It's tempting to try to bring the workflow you're familiar with from Photoshop into your expanded repertoire, but you'll end up fighting InDesign instead of working with it. In this case, however, InDesign has a feature that's designed for working with multiple layouts in a single PSD. You don't need to export anything or set up multiple PSDs unless you want to.
Instead, just make each of your page designs a Layer Comp. Show one layer group (what you're calling "folders") and hide the others, make that a Layer Comp and name it appropriately. (You want to be able to look at it a year from now and not have to scratch your head wondering which one is which.) Do the same for each of the other groups, so that you have a Layer Comp for each page background.
Place your PSD in your InDesign document and with it still selected, right-click and choose Object Layer Options.... In the dialog is a drop-down showing the currently active Layer Comp in the PSD. Change that to the one you need for that particular page in the document.
Although the feature was built with a different use case in mind (where the designer might want to give the Art Director or client multiple options for a single layout), it will work perfectly for this scenario.
