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Depends on where you are coming from. For instance Tiger Airways flies direct from Singapore into Macau. On the other hand most carriers from Europe or the US will only fly into Hong Kong.
99% of people go to Hong Kong and make a day-trip to Macau. The trip to Macau from Hong Kong is about an hour on the ferry, so you can spend five hours in Macau and still fit the whole thing in between say 10am and 5pm. Immigration procedures are straight forward, you don’t need to get a visa in advance. You certainly won’t need to ‘book out’ of your Hong Kong hotel.
IF you do start at Macau though, you can stay a night (or even two) in Macau (I’d recommend the Hotel Coloane on the peaceful Coloane Island in the south of Macau) and then take the ferry to Hong Kong. This means that you arrive in Hong Kong (for the first time) the way people have for hundreds of years – by boat. Schedule it to arrive at 8pm or so, a little bit after sunset and you will see one of the world’s most extraordinary sights. Try and get a ’superclass’ ferry ticket – better seats and better views. This itinery involves you then rebooking into a Hong Kong hotel though… as you would want to be based in Hong Kong while looking at the many sights there.
If you do make the day trip FROM Hong Kong to Macau, consider having lunch in a Macau restaurant or cafe, possibly in Macau ‘city’, or (better still) down on Colane Island (10 minutes away), and unless you want to ’see the action’ I can’t recommend the casinos (or any of the hotels near them). And avoid (if you can) travelling to Macau on the weekend or public holidays – it gets very crowded.

There is no such thing as checking out of your hotel to go to Macau. I visited both cities in November. I was staying at a hotel in Hong Kong. I just went to the port, took a ferry in the late morning. It takes about an hour. Walked around the town, gambled a bit and took a ferry back in the late afternoon.. I only did this to have a different stamp on my passport. Macau is really not very interesting

Macau is much smaller in all senses than Hong Kong and have less attractions besides the resort and casinos.
2 days 1 night is a leisurely tour but you can also do just a day tour if you skip the casinos.
I would suggest you take an early ferry going to Macau & late ferry coming back, thus eliminating the time & energy wasted in all the checking in and out. Ferry service between the two cities runs around the clock with 15 minutes intervals during peak hours and 90 minutes intervals for late night/early morning schedules. See the following links for details.

1 full day or 2 days 1 night should be good enough for a trip in Macau. The easiest way is to stay in Hotel in HK, and take an early ferry to Macau, and return to HK with a late night ferry.
The price of Hotel is cheaper in Macau. (a 5 stars hotel price is similar to 3 stars hotel in Hong Kong – very depends on season and location in HK.)
If you want to get the best value out of your money, Here is what I have done:
- Get round trip air ticket from HK airport (it is cheaper if you come from US.)
- Check out from hotel in HK at the morning of the last day that I want to stay in HK, and go to Macau/HK ferry station. (I have chose to deposit my luggage at the ferry station, and went to area like HK peak and central of HK on the same day as I went to Macau. It is nearby the ferry station.)
- Stay in Macau to the day that I need to return US.
** Take ferry directly from Macau ferry station to HK airport. The ferry only takes about 1 hour from Macau ferry station directly to HK airport restricted area. You can refund some departure or entry tax for this as well since you are considered depart from Macau directly. HK airport is really nice, it feels in a shopping mall with lots of good food in it. The best part is the things are NORMAL price. Totally same price as the outside market. The US flight needs to arrive 3hrs before department, but it is not boring at all for staying in HK airport.
Caution part:
- The ferry runs from Macau to HK airport is not as frequency as Macau to HK island. You can check for its schedule at HK airport’s website.
- Need to book for hotel in advanced. (I did it from the China Travel agency website. The agency where people applied for China’s entry visa. It feels it is safer and more official. )

i say that you sould just go to hong kong and then go to Macau by boat. You can go to a local travel agency there and buy like a tour package. It provides accomadations and boat tickets to the small island.