I’m a local, and i’d recommend staying in Yountville (9 mi north of the town of Napa). Super charming, great restaurants, surrounded by wineries and vineyards. My favorite restaurant is there, Bistro Jeanty.
I wouldn’t stay in Santa Rosa, i am not a fan at all. If you have to choose between SR and Windsor, i’d choose Windsor. Much, much nicer than Santa Rosa with some good restaurants. Windsor is a nice, very small town, not any more suburban than Santa Rosa, but smaller and has some charm, imo. But of all of Napa County/Sonoma County, Yountville is the nicest town to stay in imo.
If you are in Windsor, check out Fleur Sauvage. An amazing artisan chocolate/pastry shop.
https://www.fleursauvagechocolates.com/
If your time is short, i wouldn’t take time to visit Santa Rosa, or the town of Napa. I’d focus on… the town of Sonoma, Yountville, St Helena, Healdsburg and Windsor.
Driving the Silverado Trail is lovely. And yes, Hwy 12 is very nice. Also River Rd from Windsor to Calistoga/St Helena/Yountville