i use the apogee ensemble with logic prox and have had four mics via xlr or 4 instruments via the hiz inputs utilizing the aggregate and multioutput aspects.
sometimes it may be the order in which you choose the items. i usually start with the apogee software and then open up logic. then, i can choose my aggregate and multioutput. note that i do have my multioutput set for front and/or rear monitors so that may not apply to you. i always run in 24 bit, 44.1khz.
here is an apple link that may help you set this up better, even tho you do have it working fairly well.
hope this helps.
play music!
https://support.apple.com/en-us/HT202000