You probably want to have an evening departure from Baku (from the new bus station: head to 20 Yanvar metro station and then ask around), spend the night in Quba and leave as early as possible on the second day to have a chance to find co-passengers. The ride to Xinaliq can be expensive (maybe 40 USD one way?). There are options to sleep up there - just ask around. Expect to pay around 20 USD pppn, more if you are on full-board. One night is enough up there, but if you want to hike around, two nights may be a good idea. Quba is worth half a day for the Jewish district across the river and a couple of mosques.
For just a weekend, one is recommended visiting Lahic instead of Xinaliq. All though Xinaliq is more beautifull than Lahic, it is quite difficult to visit it from Baku in just a weekend. You will see yourself two days on the road and one night sleeping in Xinaliq. Lahic is much more easy, take a bus or marshutka to Ismayilli and from there a shared taxi will get you to Lahic for 3 manat, or a (very slow and old) bus gets you to Lahic for 1.50 manat. The busride is quite some expereince though, so a suggestion might be to take the taxi one way and get back to Ismayilli by bus.
Xinaliq is going to be too much hassle, as you will arrive somewhere in the afternoon in Quba (from Baku) and then you have to find a driver who is willing to take you to Xinaliq. Most 4WD's leave Quba in the morning, so Xinaliq will be impossible or very expensive (40 manat for a vehicle). Doing both places is impossible in two days, because the road from Lahic to Xinaliq is only possible by foot or horseback and you probably need a guide as well (distance is about 40-50km).
As to accomodation, you don't have to stay there, more options including mini-hotels available in nearby Quba and Ismayilli. If you do want to stay in Xinaliq, they will put you in someones home for about 20 manat, a bed in Lahic has a similar price. You can stay in Quba in Hotel Quba, which is 7-10 manat for a room. In Ismayilli it is going to be either Hotel Niyal (4 manat, but awful conditions) and Talistan Motel (6 manat, reasonable place). But generally ask around.
If you are running out of time Xinaliq can be a problem if you are planning the visit yourself. If coming with prebooked tour this might be easier as it will save a lot of time for transport and arrangement. For a proper visit that you plan yourself you need 3 days. First day arrive in Quba (pay a visit to jewish part of the city 'Krasnaya Sloboda' over the river). Second morrning appear at the Xinaliq bus station and ask for jeep going there. Most likely you will be were offered a ride in shared 4WD 'Niva' or 'UAZ' for 10-15 manat (one way). But you maybe you will be overcharged if you speak just English. Drivers can even drop you at homestay in Xinaliq, people there are generally friendy.
Finding a homestay is easy enough in either village just by asking around though if you don't speak Russian/Azeri/Xinaliqi/Lahici etc then Lahic is easier as at least one homestay place has English speakers.
If you're planning a trip to Azerbaijan you may be interested ▶ Azerbaijan highlights - For those who prefer to go unbeaten path, to explore less visited places and check national charisma of this small country in Southern Caucasus on the edge of Europe.
