Imagine a 1 volt battery and a 1 ohm resistor, connected to each other. One amp will flow through these two components, I call the current coming out of the positive terminal of the battery positive current of 1 amp. If it is a current source, the current out of the positive end of the source is positive current. Not sure what you mean by affect when choosing current direction. Remember, how you model something has no influence on how it behaves. #2, if you have a circuit with loops, Kirchoff's current law has to work, current going into a node must equal current coming out of a node, series components have the same current in them.