Is there a way to partition USB flash drives, so that both/all partitions appear in Windows?

Will U3 Tool do what you want? http://u3-tool.sourceforge.net/ You can modify the CD part of a U3 stick to be larger and have different ISO images. Not sure how to set it up to boot from the stick though, according to the info here https://en.wikipedia.org/wiki/U3_(software) it can be set up that way

You can partition a USB Flash Drive by using Bootice.You can also access each of the partitions one by one. http://agnipulse.com/2011/11/partition-usb-flash-drive/

If you want all the partitions to appear in Windows, then you will have to use Filter Drivers. http://agnipulse.com/2012/03/filter-drivers-removable-media-fixed-disk-windows/

Using filter drivers your USB Flash Drive appears as a USB HDD. You can then partition it using Windows Disk Management.