I like to start by putting my schematic in front of me. You generally want your parts to be arranged in such a way that the traces don't have to go further then they need to.
Usually when people make schematics they try to make their schematics "pretty". Laying your board out in the same manner as your schematic is usually a very good start. But, before you do that, look at anything that you will need to actually interact with, USB ports, programming ports, buttons, etc and put them where would be best for the end product.
Once you have your parts laid out, start by routing the most important traces. These traces are ones that have high speed data on them and you would prefer for them to not be jumping to different sides of the board.
After you get those traces laid out, route your power traces. By this point you should be able to figure out how to best route anything remaining.
It usually takes me 3 or 4 iterations of laying out a board before I am happy with what I have made. Every time I do it, I learn particular ways that traces need to be routed to make the routing simpler.
As a final note, if you have the ability to, be willing to change what pins connect to a peripheral. For example, if you have an LED connected to a microcontroller, you should try to use a pin that is the closest to where you want the LED placed on the board. Many times you don't have this freedom, but it is something to try to do if you can.