Using a two stage fermentation requires a good understanding of the fermentation process. At any time, racking the beer can adversely affect it because of potential oxygen exposure and contamination risk. Racking the beer away from the krausen/yeastbed before the Primary fermentation phase has completed can result in a stuck (incomplete) fermentation and a final gravity that is too high.
It is important to minimize the amount of headspace in the secondary fermentor to minimize the exposure to oxygen until the headspace can be purged by the still-fermenting beer. For this reason, plastic buckets do not make good secondary fermentors unless the beer is transferred just as the primary phase is starting to slow and is still bubbling steadily. Five gallon glass carboys make the best secondary fermentors. Plastic carboys do not work well because they are too oxygen permeable, causing staling.
The following is a general procedure for using a secondary fermentor.
Allow the Primary Fermentation stage to wind down. This will be 2 - 6 days (4 - 10 days for lagers) after pitching when the bubbling rate drops off dramatically to about 1-5 per minute. The krausen will have started to settle back into the beer.
Using a sanitized siphon (no sucking or splashing!), rack the beer off the trub into a another clean fermentor and affix an airlock. The beer should still be fairly cloudy with suspended yeast.
Racking from the primary may be done at any time after primary fermentation has more-or-less completed. (Although if it has been more than 3 weeks, you may as well bottle.) Most brewers will notice a brief increase in activity after racking, but then all activity may cease. This is very normal, it is not additional primary fermentation per se, but just dissolved carbon dioxide coming out of solution due to the disturbance. Fermentation (conditioning) is still taking place, so just leave it alone. A minimum useful time in the secondary fermentor is two weeks. Overly long times in the secondary (for light ales- more than 6 weeks) may require the addition of fresh yeast at bottling time for good carbonation. Always use the same strain as the original. This situation is usually not a concern. See the next chapter and the Recommended Reading Appendix for related information on lager brewing.
Different beer styles benefit from different lengths of conditioning. Generally, the higher the Original Gravity, the longer the conditioning time to reach peak flavor. Small beers like 1.035 Pale Ales will reach peak flavor within a couple weeks of bottling. Stronger/more complex ales, like Stouts, may require a month or more. Very strong beers like Doppelbocks and Barleywines will require 6 months to a year before they condition to their peak flavor. (If oxidation doesn't take its toll first. I have had some pretty awful year old barleywines.) This conditioning can be done in either the secondary fermentor or the bottle, but the two methods do produce different results. It is up to you to determine how long to give each phase to produce your intended beer. When bottling your first few batches, its always a good idea to set aside a six pack in the corner of the basement and leave it for a time. It is enlightening to taste a homebrewed beer that has had two months to bottle condition and compare it to what the batch initially tasted like.