Ok...you asked for it!

This exceeds the maximum length of a posting so I split it into two parts. This is part one.
The default setup in Eagle PC is designed for SMD and board houses. For home builds you will need to make everything bigger (holes, pads, vias & traces). This is easy to do in Eagle PC. Just modify your design constraints for these parameters and the Eagle PC auto router will make everything bigger for you. Now you have something you can work with.
At the design phase you can make your etchant last longer (i.e. etch more boards with a batch of etchant) by making sure you do a GND 'pour' with Orphans on. This will fill all the blank spaces on your board with copper (either GND attached or unattached copper...orphans). This means less copper to dissolve away, and your etchant lasts longer.
- Transfer Method - Printing
You need to make sure that the toner side on the top and bottom transparencies face each other. This improves the quality of the traces, etc. To do this, I print the the 'top' transparency in mirror mode (Eagle PC supports this). Which side (top/bottom) you 'mirror' depends on what your printer thinks is 'up'.
Also, I discovered that some UV does pass through the toner during the exposure process. This means that during etching you will
remove the copper from the exposed portion of your board and
thin the copper from the unexposed (printed) areas. This thinning can be a problem. Sometimes you can tear the thinned copper trace right off if you're not careful. My solution is to use two 'top' sheets and two 'bottom' sheets of transparency, carefully aligned. This doubles the amount of toner the UV has to pass through and produces a
much nicer board (at the expense of extra sheets of heat sensitized transparency).
- Making the exposure 'Master' - Supplies
Get yourself a set of those nerdy headband magnifying goggles. This will make everything easier. Pick up some white foam core board at your local craft store to use as a work surface (~$3 USD) Pick up some double-sided 'carpet tape' at the local hardware store. This is sticky on both sides with a waxy paper covering the sticky back side. Get some masking tape. Make sure your (foam core) workspace is
well lit.
- Making the exposure 'Master'
Begin with your two 'top' sheets. Lay the first toner side down an secure the corners to the foam core with masking tape. Add a strip of carpet tape to the top edge (don't cover your artwork) and leave the wax paper attached to the back of the carpet tape. Now lay the second 'top' sheet over that and with your magnifying goggles in place, carefully align the artwork. With one hand pressing down to maintain the alignment, remove the protective wax paper from the carpet tape with your free hand and carefully affix the top sheet to it, permanently attaching the two top sheets together, perfectly aligned.
Now repeat the above process with the two bottom sheets, toner side up this time, and with the carpet tape on the opposite edge. You now have perfectly aligned double-layer top and bottom sheets.
Now tape the corners of the bottom sheets, toner side
up, to the work surface and apply carpet tape to the opposite edge of the carpet tape holding the two bottom sheets in alignment. Then lay the two aligned top sheets, toner side
down, and carefully align the artwork. Once you are aligned, press down with one hand to maintain the alignment and remove the wax paper backing from the carpet tape with your free hand and affix the top sheets to the bottom sheets.
You now have a perfectly aligned...and stable...master sheet to work with. You will place your PC board between them later for exposure.
The final step is to attach the bottom sheets, with masking tape, to the bottom pane of the glass sandwich board you made earlier (see previous posting). Don't attach the top sheets to the top pane. That won't be necessary.
Peel off the UV protective film from the top and bottom faces of the photoresist PC board blank. With the glass sandwich board laying open, place the PC board blank on the bottom sheet(s) of transparency, which have been taped to the bottom glass pane and align it so your artwork is centered on the board (this doesn't need to be precise). Now close the top transparency over your board, make any final adjustments to align your artwork and close the top pane of glass.
You now have a very stable exposure 'sandwich' which you can lay in the sun, under a florescent tube, etc. for UV exposure and not worry about alignment issues (I promise).
The instructions that come with the photoresist boards I use say expose for 8-10 minutes, 6-8 inches from a florescent tube. Since I double the top and bottom layer I roughly double that and expose for 15 minutes per side. This works perfectly in my setup.
NOTE: I do use rubber/latex gloves for developing and etching. Once both sides of the board have been exposed to the UV, drop the board in a bath of developer (I use about 500ml in a small, resealable throw-away container). Use a small foam paintbrush to delicately brush the board as you watch the board design slowly appear before your eyes. I turn the board over every 30 seconds. After 2 minutes, I remove the board from the developer bath and rinse under cold water. You can now save your board for later if you want, but I etch immediately afterward.
When you are done, reseal the container and save the developer for your next spin of the board.
End of part one...[/list]