Depends what you're trying to do/where you're coming from. Typically painted hills and John day fossil beds takes about a day to check out, mostly because of drive time.
if you're coming up 206 from I84 and have a couple nights to blow, I suggest....
FILL YOUR GAS TANK IN BIGGS!!
For lunch, either the Indian food cart in Biggs (it's amazing) or The Dirty Cowgirl in Wasco.
Stay the night at Cottonwood Canyon State Park. $10/night, first come-first served this time of year. Right on the John Day River. AMAZING star gazing, good chance to see bighorn sheep, plenty of hiking. Hot showers year round.
From there, you'll hit Condon. Great little town. Fill your tank again here, it'll be miles before the next gas opportunity. The drive in has good food. Two boys market is a good stop if you need groceries.
Swing into Fossil, Oregon just up the road (it's on your way) stop at the high school, at the back of the football field is public fossil digging. Pretty easy to find plant fossils. Never really see people there, but a cool opportunity. The mercantile is a pretty cool building too.
Skip the Clarno Nut Beds. It's out of your way and not worth the stop.
Next town is Spray not much to see.
From there, you'll hit the Blue Basin unit of the Fossil beds. Check out the interpretive center first. Amazing center that will walk you through the history of the region with examples of fossils. Really nice bathrooms too.
You'll then want to backtrack a couple miles to the blue basin hike. Do the lower hike, couple miles. Impressive. You walk through a turquoise canyon of clay. It's just...super cool.
there's a couple hikes in the area, might as well do them.
from there you have a decision to make. Go an hour to John Day, check out the town, kamwahchung (very cool interp center centering around the Chinese influences during the gold rush) and can stay at Clyde Holiday State Park, or go the other way and hit the Painted Hills. If you go to John day, stop in If you hit Painted Hills, stop in at Mitchel and go to Tiger Town Brewing. Good food and drink. Painted hills has a few hikes to do, but not a huge time suck.
From there it's a stay locally. Unfortunately I'm a bit at a loss for recommendations overnight that way.
heading home, head through the ochocos to Prineville, then wherever from there.
Keep in mind the roads are getting icy, check the weather before you go. Services are few and far between and cell service is spotty at best. Come prepared. With the short days this time of year, you can easily fill 3 days.