This sounds like the french 3D animated kids cartoon Linus et Boom (Warning: TV Tropes link) (called My Giant Friend in English).
The story is about a group of friends who are joined by a big red alien (the titular Boom) who goes on to live with Linus (the red haired kid). Most episodes involve a new alien arriving on Earth, being chased by the evil agents (there are 2, the incompetent buffoon and the competent femme fatal), and finally Linus' group saving the alien and sending them back home through a portal.
The link to above to TV Tropes gives some more insight into the points you mention such as the main character having a crush on the most popular girl in school and her in turn having a crush on the red alien.
Set in 2042. The vaillant members of the Space Development Center (SDC) protect the Earth against those evil aliens who want to invade, control and eat innocent citizens...
Well, at least, that's what they'd like you to believe. Truth is, under the rule of Number 9, the SDC collects and enslaves any alien who has the misfortune to land or crash on Earth, turning them into Living Weapon, in order to one day rule the whole galaxy.
When a big red alien named Boom crashes on his balcony, the 12-year-old Linus has to hide him from the SDC. Thanks to the Dr. K, Linus acquires the Scire Swatch which allows him, among other things, to put Boom under a human disguise at will. His friends Iris, Monroe and Taki soon join him in his mission to find aliens lost on Earth, free or protect them from the SDC, and safely send them back home. All of this while avoiding Chase, the most feared agent of the SDC. Things gets more complicated when Jenny, the girl Linus is in love with, develops a crush on Boom.
Of the 4 kids, one kid is the main character with orange hair, one is a girl with a cap and pink dress, one is a black boy with an intelligent mind, and another is a funny boy with a green dress. The red alien looks like a cartoon bear and can transform into a kid, but with a big personality.
See the image below; from left to right the characters are: Taki, Iris, Monroe and Linus. The red alien is Boom and the little alien things on his shoulder are the Beebees.
The organisation appoints 2 agents, one man and one woman to kill the red alien.