A molten salt reactor(MSR) is a nuclear reactor that uses molten salts as a fuel instead of the traditional ceramic based fuels. One main advantage to this is that you can run a reactor continuously, and at much higher temperatures than a conventional nuclear reactor. I think that a MSR in IC would work like the normal nuclear reactor but with a few differences. You would have two menus, a normal reactor menu, and the pipe management menu. lets go see how these two menus would work.
Lets say I wanted to make this:
http://i1309.photobucket.com/a…aktorImg1_zpsbc953f49.png
That is how it would look like in the normal reactor view. Now from the pipe management view:
http://i1309.photobucket.com/a…ktorPipe1_zps37606373.png
The inner blue and red circles mean input into or output out of the reactor. The red and blue lines mean input or output between other parts of the reactor.
This is what the reactor would look like on the outside: http://i1309.photobucket.com/a…16_084424_zpsa863f625.png
You would pump in uranium on one side, pump out uranium on the other side, and pump nuclear waste out the top.
What if I want to spread out the uranium? Well, I made an example of how that would look:
http://i1309.photobucket.com/a…aktorImg2_zps92f0e2a1.png
http://i1309.photobucket.com/a…ktorPipe2_zpsb1deb0ea.png
Don't forget, not only can you pump uranium through pipes, but coolant as well:
http://i1309.photobucket.com/a…aktorImg3_zps34ec3fed.png
http://i1309.photobucket.com/a…ktorPipe3_zps5f2fad74.png
Thank you for reading my suggestion. 
BTW. I am not very good at paint. 