Sorry for jumping late on this thread. As far as I understand you would like to run WiFi Connect on wlan1 for example. And then you would like to have another access point running on wlan0. Thus you would like to have Internet connectivity through wlan1. And your hotspot will be running all the time on wlan0.
In general WiFi Connect should be run only when Internet connectivity is still not established on wlan1. Its example start script provides some example conditions on when to run it: https://github.com/resin-io/resin-wifi-connect/blob/master/scripts/start.sh
Please let me know whether this answers your question.