Unfortunately, The only way to get a smoother ride is by running stock shocks and springs. whenever you lower, you are always going to have a bumpier ride. That's the trade-off for having a tighter suspension.
My Fleet:
'15 Ford Fusion AWD Titanium 2.0 Tutbo
'14 Lincoln MXZ AWD 2.0 Turbo
'14 Nissan Pathfinder AWD SL
'05 Pontiac Vibe AWD
I think you should look into using Monroe OESpectrum Struts and shocks. They are supposed to give you a less harsh ride but still give good handling. They are a newly designed shrut. They do have them for the older 2003-2008 Vibes. I am waiting for them for the 2009-2010 Vibe. I too, want a softer ride.