I will be picking up two packages of bees this weekend and installing them in two adjacent hives. I have installed single packages many times, but never two at the same time. When installing a single package, after shaking as many bees out of the package as possible, I put the box on the ground in front of the hive and the remaining bees in the box find their way into the hive. I am concerned that if I do this with two packages and set two package boxes next to each other in front of their respective hives that the bees might enter the wrong hive. Is this a problem? Is there anything I can do to prevent it?
Since you only have two packages to shake, choose the evening (after the sun has set) as your preferred time.
By your description, you try to get most of your bees out. So from my experience, the actual bees remaining stuck inside the package is insignificant.
A small mist of very light sugar syrup helps when pulling the queen cage out.
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What you could do is turn the entrances 45deg away from each other, forming a 90degree angle. That distance between the entrances should be great enough to remove any confusion, if any. Then after a while return the entrances to their original position.
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I agree with @Doug1 - the key is to install them around sunset, but before dark. That way you won’t have as many bees doing orientation flights right away, and they can spend the night getting used to the smell of their new home.
The other thing to bear in mind is that package bees have usually been with a queen in their cage for several days. As queens are not cloned, they smell slightly different from each other. Once a package has accepted their queen, they will all be looking for her scent. As long as they have had enough time to fully accept her, they will be flying into the hive with a queen that they recognize.
Using @JeffH’s suggestion in combination with @Doug1’s points, you should have a good result. I have not needed to rotate the hives, but I have installed 3 packages at once in adjacent hives with no big problems. I always do it late in the day though, and as with nuclei, I let them settle down for an hour or two before I put them in the hive.
Good luck, and please let us know how it goes! 
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Thanks to everyone for all the great advice. I pick up the packages Saturday morning and will plan to install at dusk. Unfortunately, each hive has its own leveled and anchored cinder block stand that won’t allow me to rotate the brood boxes/hive entrances away from each other.
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Here are a few other suggestions that you may, or not decide to do…perhaps you are using some of these ideas already.
It’s important to “put the bees to work” as soon as possible…after all, swarms do have an incredible work ethic, and packages are just artificial swarms.
In my climate, I have found these management tools important:
Use an insulated top cover. This allows extra retention of heat in the hive so the bees can process sugar syrup and build out wax.
Use a layer of 6mil poly plastic on top of your brood frames. In drier climates, keep the brood nest humidity elevated and get a good seal on the hive top so no heat is escaping.
Provide extra nutrition for a couple of weeks after installation, even though you may have feed frames already installed. You never know with spring conditions, and you want a steady food supply in case the weather turns cold for a week or so and foraging halts.
The photo above illustrates a protein patty and a frame feeder with sugar syrup. The timeline is two weeks after shaking this New Zealand 2.2lb package. Note the wax built up under the 6 mil poly.
I really don’t like doing inspections this early on queen acceptance but it needs to bee done with a minimum of hive disruption. Often the plastic may allow one to just expose a few frames at once with minimal heat loss and if I see brood in the egg or larval stage, I just close up the hive. Sometimes I have to dig a bit deeper. If the frame feeder needs a bit more syrup, I just peel back the plastic 2 inches, fill the frame feeder, and the hive remain undisturbed.
Through experience I’ve found if the hive is consuming the protein patty, the queen is doing fine.
I also congratulate you in choosing the package option instead of nucs to establish your hives. This is so important to prevent disease (AFB) and to slow varroa establishment.
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