Aligning the time Ruler

Assuming it's a fixed tempo click track, all you have to do is count out 8 or 16 measures, set the Now time at the downbeat transient (tab to transient makes this easy; you don't even have to be showing transients), and use Set Measure Beat At Now (Ctrl-N in X1 now, I think - used to be Ctrl-M) to tell SONAR what measure an beat that should be. SONAR will automatically change the initial tempo to align the time ruler.