I'm reworking a schematic for the arduino word clock in eagle (making it smaller).
I've re-jigged the schematic and started to route the traces by hand in the board layout.
my question is this... while rerouteing the tracks I have changed the relationship of certain tracks and pins (all GND's ) from the ratsnest connections to more beneficial layout ones... if i accidentally connect one track or pin wrong will the software flag it up the difference from the board to the schematic?
Not sure what you mean - you shouldn't be able to connect pins that aren't meant to be connected together without violating the fundamental way eagle works.
You can only connect things that have "air wires" between them - they are thin yellow lines. When you click the "route" button (you ARE using the "route" button yeah as opposed to the "wire" button?) and click in the window, it selects the nearest air wire.
Now it is possible to check if two unrelated tracks are too close or touching. Check out the "erc" and "drc" tools and their associated help files.
Sometimes the yellow wire for say a ground net wants join with the ground half way over the board (which i can't route). There is a closer ground that i can manually connect it to (but the yellow route doesn't see it).
if i connect to the closer ground will it affect the layout?
Firstly, try hitting the "ratsnet" button - it refreshes all the airwires, and will pick the closest one. If it's not seeing the closer one, check that both traces have the same name. You can do this with the "info" tool, which looks like an eye.
Sometimes though you don't want to route to the nearest location. In this case (and what you can do if it's not picking the right one in general) is start the route, then manual route close to the location where you want to end up. The air wire should snap to the desired location if it is a valid target. If that doesn't happen, again check that the traces have the same name.