Everyone in my immediate family has male dogs: my parents have a 4-year old boxer, my sister has a 2-year old mini pinscher/terrier mix, and my wife & I have a 12-year old pug. All 3 dogs are neutered and have been for some time. The boxer is a rescue, but has lived with my parents since he was about a year old. The pug is also a rescue, but that was 11+ years ago.
When we get together, we like to include the dogs as much as possible, but we rarely get all 3 dogs together as it becomes a chaotic mess with 2 young high energy dogs and a 3rd mellow, older dog. Generally speaking, everyone gets along fairly well in pairs.
The boxer is usually very protective of the smaller dogs (or anything smaller than him, such as toddlers). However, the boxer and the pug have a recent history of rough play (not quite "fighting" as I would define the term). Specifically, while the boxer and pug (and their respective owners) were living together for a few months, the boxer grabbed the pug by the neck scruff and lifted him in the air on 2 different occasions. After the first incident, the dogs were separated but were slowly reintegrated a few days later. About a month later, the 2nd incident happened. The pug was physically shaken after the 2nd incident, so the dogs were separated permanently the same day: the pug was sent to live with my in-laws until we moved back to our house after a month.
Since the incidents, we've avoided getting the pug and boxer together. In the meantime, the boxer and the mini pinscher/terrier mix have continued to get along with no incidents. Given there has been no sign of aggression from the boxer prior to this toward either dog, or since together the mini pinscher, we have considered trying to reintegrate the pug and boxer for short durations.
What is the best way to accomplish this?