At the back of the head unit you'll have some pre-outs for the front speakers, you just need to run some phone cables from those pre-outs to the desired channel input on the amp.
Then you'll need to run some speaker wire from each channel on the amp to each door to the speakers.
If you're fitting the amp in the boot then you'll need to remove the trim on the inside of the car to run the wires.
Check this video out -
It's an E90 but there shouldn't be too much different with regards to running the wires.
Hope that gets ya started, it might seem a little daunting but it's easier than you might think!!
Just take your time and get a trim removal kit, maybe some spare trim clips......