i have read the thread, and understand the related technology quite clearly. there is a bit of mis-information in this thread... bongo as usual nailed it, but many others did not... sorry if i made things worse, let me try to clear it up.
an effects loop in an insert point in the signal chain of an amplifier. you plug your bass into your amp, it goes into the preamp. the EQ is part of the preamp circuit, generally. an effects loop gives you a point to 'pick off' the signal between the preamp and poweramp. the fx loop send is essentially the output from the preamp, and the return is the input to the power amp. many fx loops have a mix knob, but not all.
the chorus pedal thing is basically people saying that they prefer hearing the chorus happening AFTER the EQ-ing of the preamp.... as opposed to EQ-ing a chorused sound (probably because they are boosting lots of high end and bringing up the hiss from the pedal)... i don't know, i hate chorus.
what i am saying (which is the same as what bongo was saying) is that if you use the effects loop in the intended manner, it will have no affect on the functionality of the preamp or EQ in your amp, and anyone suggesting otherwise is wrong. some fx loops may have the option to be switched pre or post EQ, but i assume that most are post... what your manual is saying is that using the return ONLY is a way to patch directly to the input of the poweramp, bypassing the first half of the amp (why i said just sell the amp and buy a poweramp...)...
to invert the concept, the fx send can also be used to split the output from the preamp, either to a DI or another amp...
more clear?
these are all basic signal flow concepts, but can be easily misunderstood... fx loops are like a patchbay in your amp... you can use the fx send only to split the preamp signal, use the send and return together to insert processors, or use the return only to connect directly to the poweramp.
john