Why would it need to be accessed from software? There's probably a strong likelihood that hardware manufacturers will configure the FPGA in the factory, and the end-user will end up oblivious to the fact it's even there.
http://www.fpga4fun.com/ is a nice site with stuff that novices can have a go at creating.
There's also a sister site (http://www.knjn.com/) where you get hold of inexpensive FPGAs for tinkering with.
There is a savings in board space, but, otherwise, this solution provides no additional value. You can already connect an Atom processor and FPGA through PCI Express.
I am not yet aware of FPGA-like chip architecture that can be reconfigured dynamically.