My personal answer to this problem was to go the hardware sequencer way. There's nothing quite like setting up a sequence then flicking the switches and tweaking other parameters in real time. The sequencer becomes an instrument in its own right.
As a dedicated sequencer (as contrasted to a synth with a sequencer built in) I use a Doepfer Dark Time, which outputs MIDI as well as cv so can drive software synths as well as hardware and the MIDI output can be recorded into Sonar like any other controller.
Which is useful because not only do you have a permanent copy of the sequence you also get to see which notes it was playing which makes building arrangements round it easier.
Sequences can also be played back pitched via MIDI notes, so if you play e.g. a C then the sequence will pitch to that, a G and it pitches to that and so on, so it can follow the harmonic progression of the rest of the music.