Sorry late replies...
Mark - no you can not put in the thermal bridges very accurately, in fact the u-value calculator is not brilliant either and this is one of the bad points of IES. In terms of the level of detail you currently look at in relation to bridges and junctions, the model is a little bit more basic. To accomodate you would have to adjust u-values to take into account thermal bridges. For residential I use another program which links the geometery from IES into a SAP program which has a better U-value. Thermal bridges can be entered on that but this is a manual entery.
Nick - I think this touches a little bit on Marks point. The level of detail in the thermal modelling does not match the level of detail in relation to PHPP. For instance, although shading, orientation, ventilation, glazing etc can be modelled, different frames become difficult. For instance, when looking at solar control glazing, I have to look up the glazed units on Pilkington to obtain the various short/long/shading coefficents etc and then adjust the parameters of the glazed unit within the model to get the same details. However I am guessing that if a material is not in the PHPP database you would need the details to enter in a a user defined material anyway. Coming back to frames, there is a selection for frame types however you are better off looking at the manufacturers window unit data and entering that data into the materail database rather than trying to "custom build" the unit within the software.
I am working on a project at the moment with an AECB architect who has already put the buildings through the PHPP software, so hopefully I will have the opportunity to compare. Alternatively if anyone has a small simple project they want to compare then please let us know - I think it is useful to compare a "real life" project.