I've just brought a new water pump, might sound stupid but what pipe goes to the inlet on the back? I might be missing a hose...

Pipe at rear continues straight out under RH Extractor to end of engine, then rises up to meet heater nipple at bulkhead. Keep hose between dipstick and eng block and ensure clip at cyl head holds hose securely:
I added a Zip tie to the Head Clip to annoy "Murphy" and save a burst hose !

I hope your new pump has "GMB" stamped/embossed on it somewhere, or at least "Made in Japan"
These are the only ones I know will outlast your lifetime if you run 50% concentrated coolant with 50% distilled water
Bernie
 

BEE VEE
Pipe at rear continues straight out under RH Extractor to end of engine, then rises up to meet heater nipple at bulkhead. Keep hose between dipstick and eng block and ensure clip at cyl head holds hose securely:
I added a Zip tie to the Head Clip to annoy "Murphy" and save a burst hose !

Okay my heater appears to have been blocked off, will have to reconnect it at a later date. To start with I want to try and start the engine.

It's a Gates water pump, comes with 2 years 40000 km warranty, appears to be a quality product.

If you have a water heated Choke as per normal, run heater hose as I prev explained, but make it continue past heater pipes over onto intake Manifold Rear Nipple. 
The WP front/upper 1/2" outlet hose can go to your Water heated Choke and then back to Thermostat 1/2" nipple, assuming your choke water nipples are both facing front of car.
If Heated Choke has been deleted, then just run "back of WP" hose as prev explained, plus the other 1/2" upper WP nipple hosed to the Thermostat 1/2" nipple.
 
"Waddaya rekin ?"