It seems to me that you are doing things the hard way. Your httpd.conf file should not be large and there should only be one .htaccess file per site. As well, you are under the impression that .htaccess files are inefficient which is not really the case.
Using config files requires the Apache server to be restarted in order for the configuration change to take effect. For some features, such as redirects, where changes can be frequent, this is not recommended. Httpd.conf and the various site configuration files are not the best place for some configuration work.
Traditionally, this would be left up to the .htaccess file. Only one per site is necessary since references to sub-directories and such can be made from the one file. If you were creating multiple .htaccess files per directory within the www directory, while this is fine to do, it really is unnecessary and harder to manage as you said.
As far as .htaccess files being inefficient, this is a bit of a misnomer. There is a slight additional burden of accessing an additional file for configuration, however, this burden is extraordinarily light and should not be a consideration. Other than that, the .htaccess file is no more inefficient that any httpd.conf file. The process is exactly the same except that using an .htaccess file does not require restarting Apache. This file is poled periodically and configuration changes applied automatically. This happens rather efficiently and quickly.
You used the term virtual server. This may mean something different to you than it does to me so I am not exactly clear what you are referring to. For this reason, I am assuming you mean another website using virtual hosting methods.
Traditionally, virtual websites are created under the home directory each with it's own directory. Lately, some configurations like to create one main site and other site directories under that. I do not recommend this for security reasons. It is possible to secure this, but it comes at a cost. In the traditional method, you would create your web space under the home directory for each site you have. Then you would create under that a www, log, and any other directory you need. This is where I create any cgi-bin style directory for example. This avoids other security issues with having it in the www directory. You would then use the sites-available directory in /etc/apache2/ to create your virtual hosted sites. I will not get into the details of this since it is a broad topic and if you have a control panel, much of this should be handled for you though some control panels configure Apache sites differently.
My recommendations are simple. Static configurations go either in the httpd.conf file or in the case of virtual hosting within a site configuration file using the sites-available directory. As well, all ad-hoc configuration changes would be made to the .htaccess file within the www directory and that file would contain all the configuration for the site.