I have finished several schematics in eagle 5.11 which I used the Wire tool to make connections, I recently found a tutorial that said not to use Wire but to use the Net tool to make connections, is there a difference and if so what is the difference and why does it matter?
Should I go back and redo my schematic part connections with the Net tool? Will it make a difference in anything?
Oh boy...big difference 
The Wire tool is really a documentation tool. You can use it to draw boxes, annotations, etc. But only the Net tool has electrical meaning. When/if you go to route your PCB you will see no "airwires" because you have made no electrical connections.
To fix it:
disp none wire (display no layers except wire)
group (select all your wires using the mouse)
change layer net (after typing this, right-click to apply the change command to the whole group)
disp all (display everything again)
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Thanks again rugged but now I am confused a bit more I do see airwires on the PCB, little yellow connections between each component. But I will fix them anyways.
Did I mention I hate counter-intuitive interfaces.
I really wish I could just take a class, but I have been stumbling along for almost a year now, trying to figure it out by myself, I could have made the board the old fashioned way I used to as kid faster, using tape outs, than this damn "timesaving" cad can.
But of course then I would only be able to etch my own and not get it commercially produced.
Once again your help is greatly appreciated.
Oh and even more confusing the autorouter works on those connections.
Some things do get lost in the German-->English translation.
Here's my Eagle cheat sheet:
CUT means COPY TO PASTE BUFFER
GROUP means SELECT
WIRE means LINE
NET means WIRE
MIRROR means MOVE TO OPPOSITE LAYER
INVOKE means ADD ANOTHER GATE
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Thanks Rugged, but this is an Eagle gotcha and half for both of us, it turns out, at least in Eagle 5.11 and maybe others, that the wire tool converts connections between parts automagically to nets.
When I typed the command disp none wire I got an Unknown Layer wire error, even though I did draw the whole schematic with the wire tool, and when I type disp none nets it shows all of the wires as nets, go figure.
So I guess the answer is to be correct use the Nets tool for parts connections, but if you mistakenly use the wire tool it will convert connections to nets, but this should not be relied on behavior.
Neat! Having used Eagle from the v3 days some changes just don't register. I'm glad the wire vs. net thing is being resolved.
I forgot there is no "wire" layer. It used to be that the WIRE command would draw lines on some other layer (Names? Values? Info?) while the NET command also drew wires but on the Net layer. Same tool, just drawing on different layers. In fact, if you selected the WIRE tool then selected the Net layer from the layer dropdown it would be exactly equivalent to using the NET tool. Looks like that is the default behavior now in 5.11.
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And thats exactly why its a bear learning this thing from various internet sources rather than a tutor or a class. The internet tutorials are usually a snapshot in time and don't evolve much or get updated as the program does.
Thanks again.
What about the "official" Eagle tutorials and manuals?
http://cadsoft.de/Tour/tour00.htm
http://cadsoft.de/faq.htm#06011301
I haven't looked through them for a looong time (since v3), but that's how I learned Eagle. Are they any good?
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What the "wire" tool will not do (at least in the latest version of Eagle for Linux) is automatically connect wires together, you have to manually put an interconnection. That's even if you click to start the wire on another wire! It does link parts together as long as the wire starts or ends on the part you're trying to link though.
Gives you strange warnings sometimes too, I need to try out the net tool and see if I like it better.