Eagle PCB is weird. It's kind of like Democracy:
Eagle is not great, but it's better than all the other forms I've tried for the general PCB hacker such as ourselves and our friends. I used the non-profit version for a stint, but when we started to sell our designs we took the plunge and purchased the professional version.
If you do decide to shell out the money, you'll get the opportunity to layout a board up to 16 layers! Really? You should rarely need more than 2-layers. But if you spend the big bucks on Eagle, it will by default assume you want to layout a 16-layer board.
Look at all that noise! 16 layers is great for a motherboard, but that's really not me. And all those extra layers cause lots of problems when I'm tying to route between layers. While routing, I like to use the mouse and keyboard to quickly drop a via and jump to the opposite layer (either top or bottom). This is how I route between layers:
As you're routing, hold Shift. Now when you click, because you're holding shift, it will drop a via on the board. Neato.
Now after you've dropped the via, click the middle button on your mouse - it should be the scroll wheel. If you have more than 2 layers, Eagle will pop open a window asking which layer you want to go to.
Wait! I just have a two layer board. Why is it asking me which layer I want to go to? I want to go to the opposite layer obviously! This can be really annoying. If we can convince Eagle we only want to route two layers, Eagle will switch to the opposite layer. So how do I remove those annoying inner/extra layers in Eagle? It's completely wild, but not too hard:
Open up the DRC menu by clicking on Tools->DRC. Click on the 'Layers' tab.
Checkout the 'Setup' box. This is where you can create an entire stack up of layers of various thicknesses and complexities. It's all very fancy, but if you 2 layers, it's overkill. To remove the extra layers (and just have a two layer board) remove the parentheses from "(1*16)" in the Setup box. Then click apply.
Now add the parentheses back. Yes, put them back. Now click Apply - this will cause the changes you just made stick. Then click Select - this will close the DRC window and return you to the Eagle PCB window.
Now if we look at the layers again, you should see only Top and Bottom. Yippee! We can now route quickly using the mouse wheel button to switch between layers. Enjoy!