I have gone down the timer route as it appears that having a staggered light pattern helps to prevent the growth of algae. So a few hours during breakfast, off till late lunch then on from 4pm to about 11pm, giving me around the 12 hours of light that the plants require.
Ref the junction box, i was in the same boat with all of the electrics wired into one box which had switches, one for filter and one for whatever you decided. I went to Maplins electrics looking for a device that I could hardwire in that would act as a timer. They didn't sell one as such but they said it was possible to make one out of components, as I am not not that way inclined I unwired and added a plug, went to Tesco and got 3 mechanical timers for around £5.