Not sure if these are best practice, but my workflow is something like this:
1. Draw the schematic.
2. Draw a board template. I find it easier to do this with a rectangle, in case i want to alter the dimensions of the board easily during the layout process. Then I place the proper board over it at the end.
2. Place the template so that the origin is in the centre, which helps me line things up perfectly with my Illustrator designs.
3. Lay out hardware that must correspond to an external drill hole or component (e.g. pots, switches, DC input, 3PDT breakout pads etc). I always specify an exact location for these rather than dragging or using the dimension tool, which I find inaccurate and messy. I also place things like ICs centrally and evenly spaced from each other too. Pads for 3PDT, DC and jack ground are on 2.54 mm centre spacing so that screw terminal blocks can be used if desired.
4. Go through the schematic and firstly complete the LED path and the power paths. Some people use thicker traces here (0.33 mm) for heat dissipation on the power path and thinner ones (0.2 mm) for the audio paths.
5. I then highlight each net, lay the compnents from it out on the board and add the traces. I dont care much about the schematic or ratlines at this stage, just the nets. I ignore the ground net, as I use copper pours as ground planes. I usually get better results if I do traces as I lay out the components, although there is still a lot of stuffing around re-working traces if you do it that way. I used to do layout and tracing as distinct steps but I found it worked less well and I have a bunch of aborted layouts from that time. I always hand-route, although i will sometimes run the autotracer to get ideas about tricky parts. I try and route horizontal traces on the top layer and vertical traces on the back and connect these by vias if necessary for tricky sections (I think I read it's called Manhattan routing?)
6. When I'm laying out components I try to take many leaves from our good proprietor's book and attempt to put runs of resistors in an inner column along either side of the ICs with caps in outer columns, at least where possible. I aim for some degree of symmetry where possible but do not possess Mr. PCB's grandmaster skills. I use DipTrace's alignment and spacing options a lot to get things nice and balanced in each column.
7. After layout and routing, when I'm happpy where everything is, I rotate or move the component labels for the silkscreen.
8. Set up copper pours on top and bottom and connect to ground plane (although sometimes I'll have a power plane on top if I have multiple positive voltages)
9. Place board outlines leaving the required space around the edge of the copper pour. Add vector artwork labels. Remove the board template shape.
10. Important! Check 3D rendering! I have caught so many mistskes by checking the 3D model of the PCB.
Would love to hear any tips others have. Here are 3 boards I've made recently for a custom bass effect I'm building for a work colleague (resonant lowpass filter, fuzz and boost).