That's probably Linus et Boom (2009), a French-Korean 3D-animated cartoon, known in English as My Giant Friend.
When a big red alien named Boom crashes on his balcony, the 12-year-old Linus has to hide him from the Space Development Center (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.
Indeed, the big red alien gets injected "an electronic chip, specially prepared to be controlled by your [Linus'] watch", as you can see in the episode below (2'17):
The organization (the SDC) is indeed catching aliens, and two agents are appointed to hunt Boom down: Chase and Sandborn, which you can see below, as well as some robots. You can also briefly see these robots in the cartoon's intro, for instance.
The Scire Watch can open a portal to the aliens' world, as you can see in the following episode, at 5'5 (in French, didn't find an English dub for that one):
Found partly by luck, since someone had posted it as an answer to another question, and as always when another ID turns out to be French, it stuck in my mind... Saw the alien thing here, figure I'd give it a try, sheer luck!