In the episodes, the monsters and aliens are shown getting along, sometimes even becoming friends!
It appears that all of the monsters are paired up with an enemy alien, after all, there are four members on each team! Susan seems to have to be arch enemies with Vornicarn, but she could be enemies with Coverton as she seems to hate him more than B.O.B does, but Coverton hates B.O.B more than he does Susan. So far in the series, she hasn't been shown trying to "make friends" with any of the aliens, she only felt forced to bunk with Sqweep. Susan is shown talking mostly to Link, probably because they are bot the tough ones, but also because Link's the only sane monster that can remind Susan the consequences or lay things down straight to her, but sometimes, this relationship is shown with Dr.C.
Dr.C seems to be arch enemies with Sqweep, as shown in the episode: It Happened On A Field Trip. At first, he was shown adoring her, then being offended by her superior intellect. Unlike the rest of the monsters, Dr.C seems to have had no friendship links with any of the aliens, but his nature leads him to get along around them better than the rest of the monsters. Dr.C is seen enjoying Link's company, Link has a cheeky and sly nature like himself but is also very non-crazy and is needed to doubt and comfort Dr.c. He seems, also to like hanging around Susan because they are both adult humans in origin and far less childish than Link and B.O.B.
The Missing Link
Unlike the rest, Link is extremely attracted to his enemy, Sta'abi. He has shown his interest in her in a couple of episodes, but has also shown his hatred, telling Susan to step on Sta'abi. Link dislikes all of the aliens, because, as shown in the episodes, he is ever so slightly protective of Earth, he defends Earth from the aliens many critisisms, so is slightly more hasty have a fight with an aliens than the rest of the monsters. Recently, Link has become best friends with Sqweep in the episode: The Friend Who Wasn't There. He and Sqweep did many activities and the characters put accross a Father-Daughter or Big brother-Little sister vibe to their relationship. Link seems to hang around each of the monsters about the same amount, he loves playing with B.O.B, watching over Dr.C and playing tricks with him and talking to Susan. Link is similar to all of te monsters, but maybe in the past, Dr.C and Link probably would've had the tightest friendship in the base.
B.O.B is far too dumb to actually hate anyone, but his enemy is also his best aliens friend, Coverton. B.O.B loved explaining to Coverton what a "buddy" was and, since Coverton didn't have one, B.O.B insisted on being his buddy. Although there are occasional hints for B.O.B being Sqweeps friend, but B.O.B seems to like all of the aliens. His best friend is in many of the episodes, shown to be Link, again. Link also has a dumb childlike mind, so B.O.B finds him very relatable. B.O.B is grateful that Link "really knows him" and B.O.B even cries "Link's MY best friend! If anyone get's to eat him, it should be me!"
Coverton's worst enemy is B.O.B, he often describes B.O.B as an idiotic blob. Also because Coverton is fairly smart and had no idea what a "buddy" was. His "friend" would also be B.O.B, but Coverton makes it clear in almost every episode that he wants to destroy ALL of them. Since Coverton is the main alien, he has to like them for them to be in his team. At first meeting with both Sta'abi and Sqweep, he admired them or their work. He seems to know alot abpout Sta'abi's culture and so maybe they're more relatable. Yet he is seen wanting to get away from Sqweep and get to Sta'abi, so maybe his favourite alien is Sta'abi.
Sqweep, to many, is misinterpreted as a boy. Many claim that on the official DreamWorks website, she is claimed to be a male, yet she is only reffered to as child. In the episode; Number Seven! She is officially called a "she" by B.O.B, also in Night of The Living Dog, she is called, by Monger, Ms Sqweep. Her enemy, is Dr.C, but she isn't shown to dislike him, only overthrow him. Her friend has been shown to be Link, she, unlike Coverton, enjoys the monster's presence and is sad when Link abandons her. She is shown to want to be paired with Coverton in episodes and Coverton might be her favourite alien.
Sta'abi is shown to dislike Link, she does appreciate that he's strong, but doesn't like him and hates when he asks her out. She has no monster that likes her or wants to like her as a friend so far in the series, but Susan seems sort of fond of Sta'abi and wants to "make peace". Her favourite alien is by far Vornicarn, as her pet, he is probably the only thing Sta'abi actually cares for.
Vornicarn likes Link's nose, B.O.B and acts as a pet fro Sta'abi. His enemy might be Susan, as they are both the larger members of their team, though, he is shown to eat B.O.B.