Dear Mastersamo: your guitar signal should go into both preamps, which then will run "in parallel", although you'll use either one or the other.
Since you have another, completely independent clean preamp, you can switch between them using Led_LDR or Relays; FETs or CMOS gates aren't well suited for the high signal levels usually carried by tube preamps.
Remember to have an extra switch to kill gain on the distorted channel (besides switching it off) so as to avoid noise feedthrough/crosstalk when unused.
*This* version of JCM900 you link does not have any switching.
The one which does, is a *very* different beast, and might be considered a giant SS distortion pedal, driving a tube power amp.
Yes, it does have a tube, but since it does not distort, it doesn't add much to the final sound .