Installing one WP instance in root directory and another in a directory in root

I have one instance of WP (multisite in fact) in root directory with domain, say, rootsite.com. I have another instance of WP (not a multisite) in a directory, say, secondsite and it is mapped to the domain secondsite.com. Now I’m facing following problems because of this configuration:

My permalinks get automatically updated to https://rootsite.com/secondsite/… while I want it to be https://secondsite.com. This obviously breaks my site whenever user tries to navigate my site beyond its homepage.

Also, no matter what address I write for “WordPress Address (URL)” and “Site Address (URL)” they also automatically get updated to https://rootsite.com and https://rootsite.com/secondsite, respectively.

I don’t seam to think of any solution for this problem. Please help!