After a sharp downpour soaked the 4,445m circuit, the morning's first session produced very little action with just a few riders venturing out on track.
Checa, on a Ducati 1199 Panigale R, took advantage of improved conditions in the afternoon session to produce a fantastic lap time of 1:31.059 to top the standings.
BMW's Marco Melandri was second after registering a time of 1:31.237.
Suzuki's Leon Camier, who was 10th with a lap of 1:31.814, said: "I just kept things really steady today to be honest. This morning was drizzling, so we didn't even make a lap and this afternoon we just had a few small things to try.
"We tested the harder tyres to see how long they would last and which would be the best tyre to run, if it is colder on race-day.
"We just cruised around really and didn't try to go for any lap-times this afternoon, it was all about confirming a few things and making sure the bike's feeling was right."
Day Two Classification:
1. Carlos Checa (Ducati) 1:31.059
2. Marco Melandri (BMW) 1:31.237
3. Tom Sykes (Kawasaki) 1:31.26
4. Michel Fabrizio (Aprilia) 1:31.350
5. Jonathan Rea (Honda) 1:31.356