hi J.D., welcome to the forum!
there are probably as many ways to approach this as there are people. so take my suggestions as just a few among lots of other good ones. perhaps others will chime in with their favourites.
to start, i like to spread out the parts more or less like the schematic. i think i picked this up from aron's beginner project.
then i concentrate on putting in the traces for the signal path first. i don't worry much about ground or power supply stuff until after the signal path is done. try rotating the IC around to see what works best. i also pay attention to pots at this stage, because i want the layout to fit where the pots are going to go, usually along the top edge.
then i keep start the +9V and the GND traces side-by-side at the bottom. i run the ground trace more or less all the way around the outside and the +9v inside of that. in this circuit, VA takes the place of +9V. i treat the virtual ground (VB in this case) traces like the +9V traces. if i seem to need jumpers, then i would restrict them to these three (GND, VA, VB) because they are supposed to be relatively "quiet" traces---their voltage is approximately fixed.
you could also try looking at what others have done after you have wrestled with the problem a little. i have a layout for this circuit here
. tonepad.com has a layout. i'm pretty sure that generalguitargadgets.com does. i'll bet markm's gallery has a layout because he laid out almost everything before he retired from stompbox circuits.
hope this helps, paul