What MCU are you using? If it is CF V2, what I have done is default the QSPI_CS0 (or whatever) pin to its primary function, which will have it be asserted for each transfer, independently and automatically, by my QSPI library (you can see my library in sources/qspi.c at http://www.cpustick.com/downloads/skeleton.zip).
This works fine for most "fixed length transfer" peripherals, like EzPort or MC1320x wireless transceivers.
However, if I am talking to a SPI device like an SD card, where I need "variable" length transfers, based on interpretation of the data being transferred on the fly, I simply reprogram the QSPI_CS0 pin to GPIO mode (quaternary function) and control it by asserting it by hand, calling qspi_transfer() from my library multiple times, and then deasserting it.
Would that work for you?
You can also play with the "chip select inactive value" between transfers and spoof the assertion/deassertion, but my experience has been once I get to something more complicated than just "assert during the single transfer" (from the inner loop), it becomes easier to reprogram the pin to GPIO mode and control it by hand, in an outer loop.
-- Rich
