I visited this WHS in September 2017. I allowed 2 half days for both towns and spent a night in Baeza.
Ubeda is the better ensemble of the pair with more interesting Renaissance buildings and more to see. Baeza is mostly famous for its neatly carved fountains and the still active old university with a facade which reminded me of the Lonja de la Seda in Valencia.
You won't gain much in terms of OUV (if there is any) by visiting the church and palace interiors. However, if you have some time, I'd recommend going for the El Salvador Holy Chapel which is closed during siesta time. The highlight of my visit was the facade and square of the El Salvador Holy Chapel (photo). The church facade in a way is quite similar to the one in Vezelay, France. The UNESCO inscription plaque (with no mention of Baeza) is placed on the right hand side (closest to the fountain) of the Vazquez de Molina Palace.
In the middle of the historic centre of Baeza there is a bronze sign on the floor just after a pedestrian crossing but it is hardly recognisable. Both towns are very close to each other and both historic centres can be easily covered on foot. In Ubeda, I used the convenient indoor parking named Aparcamientos Ubeda in Plaza Andalucia while in Baeza I just parked my rental car in front of the hotel.
Both towns are quite similar to Pienza in Italy but are still not comparable to the Italian WHS. They aren't the best examples of Renaissance towns in Spain and I failed to notice any OUV. That said, they are quite off the beat track at least if you want to escape the never-ending hordes of tourist groups in the bigger cities of Andalucia.