Hi surfer99,
Prior to taking alli were your BMs regular? You should not be scared with the slow down just yet, it is quite possible that the increase in BMs during the first week cleaned you out and you GI tract needs time to create enough waste to eliminate. By staying hydrated and getting adequate fiber you should get to regular. Consistent use of the bathroom indicates that you need to decrease the fat (which you most likely have done in week 2).
You can always take a laxative if needed.
Best of health,
Sophia De Monte RPh