One of the colleges I am applying to has its own application portal on its website in addition to Common App. Should I submit through their website or the common app?
Nope! College admission committee won't look at where you're applying. They have no preference and will review your application without look at the application you use.
However, there's some things you should consider when choosing the platform you use. For example, the essay prompt in the Coalition App vs the Common App. I don't use the Coalition App so I don't know how is it like, but I heard that it's different with the Common App ones.
Pick the platform that you think will showcase yourself well. If you love the Common App prompt, use it. If you are more comfortable in using the university's own website, use it.
So neither application is prefered but one MAY be better for you. For example, iirc one school has their application + ComApp but only their app is no app fee. Additionally some of the application itself may be different. For example the UC app vs ComApp vareies wildly with how yo list ECs so its something to look at but in short one doesnt provide an inherent benefit.
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