Flyback SMPS Transformer choice
For instance, i want to use the following transformer:
  http://nl.farnell.com/bi-technologies-tt-electronics/hm42-10001lftr/transformer-gate-drive-300uh/dp/2192063


You can't use the transformer you want to - it isn't rated for doing what you want.


  Unfortunately i get stuck at the part where i have to choose the
  transformer (the bottom 3 choices from the "design" tab).


What's wrong with the design page that it produced: -



It tells you: -


The core (E16/8/5, Ferroxcube, 3C90, 570µm)
The gapping (0.57 mm)
How many turns for primary, auxiliary and secondary
How to wind them
The wire gauges


It even gives you options for using different ferrite cores - see radio buttons.

What were you expecting? You want something easier? Yes, well go to premier magnetics and choose a design for 5V and 1A (such as this one) and they do the job for you using a Power Integrations part: -



They'll sell you the transformer and provide all the info for the other magnetics. If you are still insistent on using the NXP tool then start learning about transformers so you can take the premier magnetics transformer and feed the data back into the tool.