You can have one htaccess file to deal with all URL requests. In fact, this is the best way to do it.
You need to make sure there are no Redirect or RedirectMatch directives.
Use RewriteRule for ALL of your rules.
In the single htaccess file you need to put the rules in a very specific order:
- rules that block access for malicious requests
- rules that redirect folder requests
- rules that redirect other requests
- rules that rewrite folder requests
- rules that rewrite other requests.
The order is:
- redirects first, rewrites last
- most specific first, most general last.