If you use Arctic Silver 5 (I used this not too long ago, for the first time) they give very specific instructions, such as taking a razor blade or flat edge and smoothing what little paste you have, making it flat and making it spread to the edges, etc etc...
As for the motherboard, the only problems for wires are: SATA/IDE, USB connectors, CD-ROM audio cables (if integrated audio), PSU/fans, and the "hardest" one, the case plugs. These should be very clearly marked on both the wires and the motherboard manual. Keep the manual. It's got oodles of info you will want later, when you need to look something up.