So how do I do the FPGA configuration for those PSoC devices?
Your advice boils down to "use separate tools instead of an integrated environment." That may be fine advice, but... Have you ever actually tried to put together a development environment (integrated or otherwise) for some embedded microcontroller, starting with the vanilla distributions of Eclipse, gcc, gdb, and etc? It's pretty painful.
I don't know about the Psoc devices. But to get going you install CDT (Eclipse C development tools), install GCC for the microcontroller you want to use, create a new Eclipse project, open the settings and replace GCC with the name of the compiler you want to use and the same goes for the includes and library paths. This is not difficult at all.
Having to set up the library paths each time you create a new project seems like a pain in the ass. I mean, if you're on linux, and there's simply no other options, then sure, do what you will. I prefer an IDE that works straight out of the box, and that works well. That's why I use PSoC Creator.
Unfortunately I've got a project on the horizon that involves something like 1024 or more digital output pins, so I'm going to have to make a foray into the world of real FPGAs, and their ages-old design environments.
Also, I put together a very quick tutorial on the verilog integration in Creator, you can see it here: