.htaccess in root and subfolder, each to redirect to own index.php

Have your root .htaccess like this:

Options -Indexes -MultiViews +FollowSymLinks
RewriteEngine On

RewriteBase /

RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(?!admin/)(.+)$ /index.php?u=$1 [NC,QSA,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^admin/(.+)$ /admin/index.php?u=$1 [NC,QSA,L]

There is no need to have .htaccess in admin folder for this simple requirement.