if you use a CFI flash than there is no special controler or boot loader.
CFI is a normal parallel flash device like any other external memory like sram or any other external device like a latch or a uart or what so ever.
CFI means that this device has in addition to a non cfi flash device some information about this device (the cfi table) that gets accessible when you perfrom some certain accesses to this device. also the programming algorithm is standard. there are intel and amd algorithm. if you have an cfi conform device, you "just" need to read out the cfi table, then you know what type it is, how the sectors and other structures are setup and you can pass these information to your programming alogorithm. the benefit from this is that you can replace the device with for example a bigger one and you do not need to modify your application.
cfi also means that you can buy cfi flash devices from different manufacture and use them and do not need to worry about programming (except external hardware related stuff)
what does this mean to your questions ?
there is no ip funtionality for cfi flash.
place an avalon tristate bridge, connect externaly cfi flash and sram and what ever to that interface and thats it.
no for sopc builder you just need to specify that reset is your cfi flash device and the offset where the software starts wioth its first instruction
for multiple nios designs, lets assume cpu0 reset ist cfi_Device offsett 0x0 then cpu1 has offfset 0x10000 and cpu2 has offset 0x20000 all within the same cfi device.
now you just need to tell nios flash programmer to store application_cpu0 to 0x0 the application for cpu1 to 0x10000 and so on.
we have designs with one big flash where a maxII loads the fpga from and this flash has several application inside and an addition external ARM also boots form this device.
so there is no cfi boot loader, just tell you cpu under which adr to fetch the first instruction.
the flash override is usefull when you use a device NOT from altera. Altera and its FAE recommends to use EPCS devices but there are plenty of other devices out there from spansion for example that also do the job. you just need to create a flash overide test file (there was a thread started from me, but has not been recovered by the big loss so the collection of proved devices posted there is gone)
as slacker said, epcs is just an oem or different labled chip. spansion has a device that i would bet is the epcs64 as all information you get for the epcs64 you will find in spansion data sheet. the epcs DS has only a subset of the spansion commands.
this file holds the information about you spi device id, its internal structures and then nios flash programmer reads out your device id and looks into that file and used the information from there.
you need only this tweak with the overide to store the information with a blaster for example. nios and your application will not detect that it is not an epcs device.
as you cfi is an external device under avalon control, you will not need to controll the access of different masters. nios or dma or custom ip
the only thing you must take care about is when you write to the cfi that nobody else talks to the cfi and interupts the access.
regards
Michael
EDIT : just looked at the spansion pdf link posted here. you can use this device, i use the S29GLxx Family with BGA in serveral designs. there is no need to worry about. just solder it and use it no modification, hacks, tweaks needed. this device is fully nios compatible :-)