The newest layer that forms on top is the one you want to make sure you re-use. The top layer has the newest\strongest bacteria. You can (and probably should) reuse the older layers but they will loose strength the more often they are re-used. If you have several layers and need to get rid of some, peel off the oldest\bottom layer and dispose of it.
Winter is here. The problem may be colder temperatures. Kombucha favors warmer temperatures to ferment well. Different people will tell you to use slightly different temperature ranges, but don't let it fall below 68 to 70 degrees Fahrenheit. Temperature shouldn't go above 86 degrees Farenheit. I have had the best results in the upper 70's. If you don't have a warm location, you can buy heating pads for your kombucha like these http://www.happyherbalist.com/heatingpanelspecialbuy2ormoresave30-40.aspx