Taking a reading from the turbo will show you how much its putting out and taking it from the manifold will show you whats going into the engine. Both have the pros and cons.
Measure at the turbo and you wont know if you have a leak and only half of the pressure is getting to the manifold. Measure at the manifold and you might see a nice 14psi but you could have a leak and the turbo is working its tits off to try and maintain it.
A bigger intercooler can see a boost increase of 2-3psi although thats me coming from a petrol tuning background and not a diesel one