I use s-gear - a lot as well.. when I do my input signal chain for guitar is this: Stompbox (occasionally a fuzz or compressor that I like) - focusrite isa pre-amp routed to channel 1 of my interface to record the direct signal - I take the direct instrument out of the isa 1 preamp and send it to a tech 21 vt bass pedal routed to another channel of my interface. My logic is - if you put a stomp in front of an amp - it should also go in front of s-gear. Im not afraid to record a good stomp box instead of a plug in - although Ive done both.
The thing I really like about s-gear is that it often responds very well to processing just like a guitar amp. Many other ones dont exhibit as much raw information as s-gear.Im still waiting for them to come out with something that covers the heavy genres as well as their current selection.
all that said - you should treat s-gear like your amp... and show it a good clean signal with nice headroom.
I rarely use the stereo options in s-gear and often opt for a mono out with none of their verbs, as I use other ones, such as psp's spring reverb.
If I want the verb to sound like its coming from the amp, I will put the verb before any eq, or compression. If I want to create the feel that the amp is in the same space as other instruments, I will eq and compress a little (or alot) and send a post fader send to a "Room" verb buss (or aux track)
As far as your original question - I wouldn't worry about eq on the way in - unless you have a nice channel strip made for that. I occassionally use an focusrite isa session pack, which has some nice analog features, ( a nice pre-amp, eq, and compression/de-esser section. ) Its helpful of I am working with someone else for example. However when recording myself, its often a little laborious to go through all those steps.