I'd like to visit both Wooden Churches of Southern Malopolska and Wooden Tserkvas of the Carpathian Region in Poland and Ukraine on a long weekend trip this summer (starting from Cracow Airport, and also taking in Auschwitz).

Can someone suggest a good base (or a nice pension/small hotel) from where to visit the 2 wooden churches WHS? I was considering Nowy Sacz, but some of you have done the math before, checking out all these little roads, villages and churches. So I'd like some advice on where it's best to stay (I don't need to see ALL of the churches by the way, I would give it 2 days)

We visited the churches in August 2014, either on day trips from Crakow (Debno, Lipnica Mowana) or Bardejov (the four wooden tserkvas and Binarowa, Sekowa), so that's probably not helpful for you. But Nowy Sacz seems to be a perfect base to visit the most interesting churches.
We especially liked the four churches of the Carpathian Tserkvas WHS, but Lipnica Murowana and Debno were also beautful.
Almost all of these churches were open (we failed only in Binarowa), but some of them seem to have limited opening times on weekends. Unfortunately, there is sparse information on the opening times and I am not sure if they are reliable.

I suppose you will go by rental car? If so, I would strongly recommend to use a GPS (we used the coordinates below).

From my notes from last year:

Powroźnik - Brunary Wyżne - Kwiatoń - Sekowa - Owczary: distance 74 km, 1.5 hours (according to Google Maps, was fairly accurate), it's probably possible also to include Binarowa

Powroźnik, 49 22 10 N 20 57 0 E
Brunary Wyżne, 49 32 3 N 21 2 0 E
Kwiatoń, 49 30 3 N 21 10 25 E
Owczary, N 49 35 19 E 21 11 30
Sekowa, N 49 37 53 E 21 11 11
Lipnica Murowana, N 49 51 35 E 20 31 50
Debno (Monday-Friday 9-12 and 14-16.30, Saturday 9-12, Sunday closed), N 49 27 57 E 20 12 42
Binarowa, N 49 45 25 E 21 13 40

Jarek Pokrzywnicki e-mailed me these useful suggestions:

Personally I think that 2 days are not enough for both as the area is relatively big and regardless of churches / tsekvas itself there are other interesiting places (cemetaries from WWI, castles, palaces, old towns, mountains ...) But if you want to stick just to heritage place check this site

http://www.drewniana.malopolska.pl/?page=obiekty&unesco=1

These are places from western part, probably the best place to start visiting will be Gorlice where you can stay at

http://www.willaludwinow.pl/kontakt.html

but any other village can also be ok.

When I was visiting the places I was based in Sękowa (there are many private accommodation possibilities but you should have your own transportation (rented car ? or bike - check this (bike rental in Gorlice)

http://www.ostrekolo.com.pl/wypozyczalnia/

Within 2 days while based in Gorlice you will have a chance to see 5 places from both sites churches in Binarowa and Sekowa and tservas from Owczary, Brunary Wyżne and Kwiatoń (the last one for me is the most interesting out of the 5).