Assuming you have a basic LAMP setup like the one used by the DigitalOcean One-Click application or as described in this tutorial, creating multiple wikis under the same domain is as simple as creating sub-folders in the /var/www/html directory.

First we'll download Dokuwiki itself and extract it in our home directory:

cd ~
wget http://download.dokuwiki.org/src/dokuwiki/dokuwiki-stable.tgz
tar xzvf dokuwiki-stable.tgz
rm dokuwiki-stable.tgz

Now we'll make two copies in the wiki-a and wiki-b subfolders:

cp -R dokuwiki* /var/www/html/wiki-a
cp -R dokuwiki* /var/www/html/wiki-b

We'll also need to make one addition to our Apache VitualHost. This is to make sure that certain directories are not publicly accessible on the internet. Edit the file /etc/apache2/sites-enabled/000-default.conf and add the following inside the VitualHost block.

<LocationMatch "/(data|conf|bin|inc)/">
    Order allow,deny
    Deny from all
    Satisfy All
</LocationMatch>

Next, make sure the permissions are correct:

sudo chown -R www-data:www-data /var/www/html

Finally, you can finish installation by visiting the URLs for both wikis:

http://your.ip.addr/wiki-a/install.php
http://your.ip.addr/wiki-b/install.php