Using Sonar's step sequencer is generally easier because you can see all the drums/percussion laid out in one window, rather than only one drum's sequence at a time.
You also get better visual feedback of which pattern is playing and shifting patterns around or adding or deleting repeats is easier. Each pattern can also be given a meaningful name. So laying out the song is easier.
You also get as many different patterns as you can program, while hardware/VST built in sequencers often have a fairly low limit to the number of different patterns you can store.
Having said that, I use the built-in 808 style sequencer on my Elektron Machinedrum rather than just using the synth as a module and sequencing in Sonar. The Machinedrum has a feature where you can alter the various synth parameters of individual drums on any step you want, which makes for a very tweakable synth. I also find hardware more tactile somehow, and programming within the built-in limitations of hardware is an interesting creative exercise in itself. Sometimes too many options lead to never getting anything done or, at the opposite extreme, stupidly complex drum parts that take days to do but often add nothing a simpler line wouldn't. For me at any rate.
Drum maps look daunting but are worth persevering with. The first attempt will probably be slow and frustrating, but like most things Sonar (or musically) it gets easier once you've had a bit of practice.