I've successfully configured my local machine for testing purposes so that eXists can be configured and run alongside each other, available individually on port 8080, and proxied through apache on port 80. The details of the eXist build and configuration are best discovered in my scripts in the repo, but the local configuration details are:

In /etc/hosts:

127.0.2.1	graves2-internal.hcmc.uvic.ca
127.0.3.1	mapoflondon6-internal.hcmc.uvic.ca
127.0.4.1	mariage6-internal.hcmc.uvic.ca

In /etc/apache2/sites-enabled/graves2.conf (one example for graves2, others analogous):

<VirtualHost 127.0.2.1:80>
	ServerAdmin webmaster@localhost
	ServerName graves2-internal.hcmc.uvic.ca
	ServerAlias graves2
	ProxyRequests Off
	<Proxy *>
		Order deny,allow
		Allow from all
	</Proxy>
	ProxyPreserveHost on
	ProxyPass / http://graves2-internal.hcmc.uvic.ca:8080/ nocanon
        ProxyPassReverse / http://graves2-internal.hcmc.uvic.ca:8080
        AllowEncodedSlashes NoDecode
</VirtualHost>

<VirtualHost [YOUR_REAL_IP_ADDRESS]:80>
	ServerAdmin webmaster@localhost
	ServerName graves2-internal.hcmc.uvic.ca
	ServerAlias graves2
	ProxyRequests Off
	<Proxy *>
		Order deny,allow
		Allow from all
	</Proxy>
	ProxyPreserveHost on
	ProxyPass / http://graves2-internal.hcmc.uvic.ca:8080/ nocanon
        ProxyPassReverse / http://graves2-internal.hcmc.uvic.ca:8080
        AllowEncodedSlashes NoDecode
</VirtualHost>

<VirtualHost 127.0.2.1:443>
        ServerAdmin webmaster@localhost
        ServerName graves2-internal.hcmc.uvic.ca
        ServerAlias test
        SSLEngine on
        SSLCertificateFile /etc/ssl/certs/spud.crt
        SSLCertificateKeyFile /etc/ssl/private/spud.key
        ProxyRequests Off
        <Proxy *>
                Order deny,allow
                Allow from all
        </Proxy>
        ProxyPreserveHost on
        ProxyPass / http://graves2-internal.hcmc.uvic.ca:8080/ nocanon
        ProxyPassReverse / http://graves2-internal.hcmc.uvic.ca:8080
        AllowEncodedSlashes NoDecode
</VirtualHost>

The one with an external ip address is optional, but needed if you want external hosts to be able to access the apps (based on their own hosts file being configured to point these domains at your ip). The third stanza allows HTTPS access; in fact Apache provides encryption, using the specified cert, but when it talks to eXist, it does that over an insecure local connection. If you try to have Apache from eXist's 8443 encrypted port for this, you'll get an error because eXist doesn't have a cert set up. You can still use the full :8443 port to access eXist directly over an encrypted connection. In both cases when using https, your browser will complain about a self-signed cert, of course.

With this approach, I've had Mariage, MoEML and Graves all running side-by-side on my machine. I've also finished and commented the script to roll out new eXists on Peach, and I'm waiting for RE to look it over before we actually test it. eXist 3.1 is out today and I built the latest dist from that tag.