There were 3 ways when I last looked:
Low Level VFR or using the LARS system where available.
Medium level with ATC using one of the corridors through the main UK spine system.
High level going above the majority of airways traffic, but again in receipt of a mil control service.
Happy to be corrected if anyone has more recent info.
The choice will be made based on the weather, sortie requirements, length of 'transit' and, of course, the aircraft type. As far as I recall, Typhoons tend to be happy going over the top almost irrespective of the transit length. F3s don't.
F15s tend to go at ML.
GR4s seem to prefer life at LL.
But as I said these are not absolutes.
STH