You're trying to do power control with a circuit not designed for that. It's not as simple as changing the bias of the transistor.
You need a darlington since the output of the opamp is a max of about 5 mA and you need 6 amps, which is a gain of 1000.
Usual rule of thumb is to set Ib about 5 times higher than HFE indicates. In other words, if the gain is 100 at 100 mA, then Ib is 1 mA, and you should force 5 mA to ensure a good saturation.
Re location, the one shown in the drawing is good. If you put it in the emitter, the whole design is different. Replace the transistor with a darlington, such as a TIP147, which has a gain of 500 at 10 amps.
But that is not enough, so I'd add a NPN driver between the opamp and the darlington, such as a 2N2222. However, that changes the polarity of the input, so the circuit would have to be redesigned.
The design has other problems, I'd want to re-design it before I used it. Some of the things are off:
pots should have a fixed resistor in series, so if you turn it to zero, you don't damage the parts.
741 doesn't work with inputs near the supply rails but this circuit can have that happen.
"1m" pot is, I hope 1 Megohm, improper use of symbols.
no voltage reference, so settings will change if power supply voltage changes.
If you tried to sink 50mA with an LM311 you'd kill the poor thing so the MJE2955 as a buffer is fine. You don't need any extra gain as it's a simple on/off function. Anything between 1KΩ and 4.7KΩ as a base resistor from pin 7 of the LM311 should turn the MJ on.
Try using a P-MOSFET transistor: IRF5305. You can get 6A with 4V Vgs.
The specific circuit I am going to make is the second diagram down the page on this website. http://www.craig.copperleife.com/tech/thermo/
In place of the "Relay coil, solenoid, fan etc" (i.e. the load) I want to put a peltier device, which draws 12volts and 6amps.
Firstly, how large does Ib have to be in order for the current IC to saturate? at what point does the Ic = B*Ib become irrelevant and Ic(sat) = Vcc/ Rc come into play?
Because obviously if this is at Ic = Icsat then I am going to have to have very large Ib current, right?
In addition, would placing the load between +Vcc and the collector be more appropriate than putting it after the emitter, or does it not make a difference?
Thanks for your help if you want to ask me more questions go ahead.