I know how to program, how do I learn how to wire things up?
where to put pull up resistor and why? What resistance do i choose?


Pullup/Pulldown resistors provide default High/Low value for a signal, that would otherwise be floating (All it's drivers are tri-stated). We don't want floating signals, because when fed to digital inputs, they create spurious transitions, can put the logic into undefined states, and stuff like that... Generally, anything in the order 4k7 - 20k will be good enough.


  it seems like there are randomly putted capacitors all round circuits
  and i have no idea why


Capacitors in most digital use-cases work for storing energy. Digital circuitry needs pretty stable power supply - the problem is, the switching inside these very circuits creates very rapid, short and repetitive power draw. This is dealt with using filtering, blocking and decoupling capacitors. They are all in parallel on the same power rail, but differ in size, ESL, ESR, capacitance, etc...


  i dont know what to do in order to not blow up processor


You read the datasheets. Right pin connections and stable power supply is good for starters.


  that crystal trick that generates clock .. how do i compute the
  numbers?


Crystals come in a) specific frequencies and b) specific load capacitances. They generally need a pair of load capacitors connected between ground and each end of the crystal in order to work properly. Again, the IC's manufacturer will likely provide you with equations/tables for getting these cap values.