Other than Environmental Engineering, which is in CALS. There isn't much cross over in major fields of study between the two colleges.
So -- if your application sets up like one for an engineering student -- heavy on STEM, etc. and you apply to CALS, you're likely not to come off as a good fit. Similarly, if you're missing what most engineering students have (less STEM, lower SAT-M, etc.,) your application won't read well.
You should apply where your interest lie.
Having said this -- I know the data is published somewhere, but haven't looked it recently. From Memory -- Engineering has higher average SAT scores and a lower acceptance rate than CALS.