From the experts at Park Tools:
Patching an Inner Tube Using a Vulcanizing Patch Kit
Glue type patches require the application of a thin layer of self-vulcanizing glue on the tube before the patch is applied.
To fix a flat, first locate the hole in the inner tube. If possible, re-inflate inner tube to at least twice the normal width. Inspect for air leaks by holding tube close to the sensitive skin of lips or by holding tube near your ear to hear leaks. Move the tube around its circumference. If you find one hole, keep looking for more. Inspect inside the tire for sharp objects or glass. Also inspect the rim strip in the rim. It should not have any holes around the spoke holes and should fully cover the holes
If you plan to repair the inner tube, use a marking pen to mark hole. Make four marks, one to each side of hole. Do not mark close to hole, as the mark may be sanded off.
1.Locate hole marked during inspection, as described above.
2.Using fine emery cloth or sandpaper, lightly abrade area around hole. Abrade an area larger than patch size.
3.When possible, clean area with alcohol and allow it to dry completely.
4.Open glue tube and puncture seal. Apply thin coat of glue and spread evenly around hole area. Spread area of glue larger than patch size. Use a clean finger or back of patch to spread glue evenly in a thin layer. Do not apply too much glue. Glue layer should not appear "glopped" on.
5.Allow glue to dry. This may take several minutes. Test by touching only perimeter area of glue, not where patch will contact.
6.Peel patch from patch backing. Handle patch only by edges.
7.Center patch to hole and lay patch on tube.
8.Apply pressure to patch, especially at edges.
9.If possible, maintain pressure for several minutes.
10.Leave clear plastic cover on patch, do not peel up.
11.Mount tube inside tire and inflate.
Also Sheldon Brown has a how to guide.