Protection not working with Wordpress

I'm building a Wordpress-based site with two separate WP installs. One WP install is at http://mysite.com and the other is http://mysite.com/members.

I've installed aMember in the public_html folder. The http://mysite.com is going to be public with no protections. I'm trying to protect everything in the http://mysite.com/members folder (which includes a vBulletin install which will be protected as well).

When I try to protect folders for http://mysite.com/members with htpasswd I get an error saying that the .htaccess cannot be modified by aMember. If I first delete the .htaccess file (which is for the WP install), I don't get an error when I go through the htpasswd setup, but then I get a 404 error when I try to go to http://mysite.com/members.

If I change .htaccess permissions to 777, aMember rewrites the .htaccess, but removes the WP info, so again I get a 404 error when I try to pull up http://mysite.com/members.

I am COMPLETELY new to this so I'm not sure if I've even installed aMember in the right folder. Should I have installed it in the /members folder since that's the folder I want to protect? Do I need to move the WP install into its own folder so there aren't two .htaccess files in the /members folder? I am so thoroughly confused.

I purchased the vBulletin plug-in since I want members to be able to log in once and have access to both the WP member site an the forum. I did NOT, however, purchase the Wordpress plugin since I'm not going to be using WordPress user accounts at all. My main database for users will be aMember. Is this where I'm going wrong? Is the WP plugin necessary to protect folders with aMember?

Thanks in advance.

The way i would do it:
yoursite.com/ root with a sales page etc..
yoursite.com/members where you place amember
yoursite.com/access where you place your wordpress and forum etc..

The amember httacess will protect the folder. Theres no reason to use permalinks for SEO since the bots cant get in there.

David

@davidm1 -- there are other reasons to use permalinks besides just SEO. Easy of linking pages and posts. Easier to remember URL for your members. There has to be a solution to this.