Normally it shouldn't be necessary to have multiple configuration files for the mapfish print module because you can make multiple layouts in your config file (with optional parameters) which you then post to the pdf/create.json URL. This page has some info (although it's a little outdated): http://www.mapfish.org/doc/print/configuration.html. In essence you can just add multiple layout descriptions like this:
layouts:
{LAYOUT_NAME}:
? : Mapfish-print.pdf MF_V1.2
? metaData:
? {METADATA_DEFINITION}
? titlePage:
? {PAGE_DEFINITION}
mainPage:
? rotation: false
{PAGE_DEFINITION}
? lastPage:
? {PAGE_DEFINITION}
{...}
(note: use ! in front of a parameter to make it optional)
The only way to have multiple configurations (that I know of) is to have multiple print links which all use a separate config. You can do that by editing the /usr/lib/apache-tomcat/webapps/print/WEB-INF/web.xml file and add more servlets:
<servlet>
<servlet-name>mapfish.print2</servlet-name>
<servlet-class>org.mapfish.print.servlet.MapPrinterServlet</servlet-class>
<init-param>
<param-name>config</param-name>
<param-value>your_2nd_config_here.yaml</param-value>
</init-param>
</servlet>
<servlet-mapping>
<servlet-name>mapfish.print2</servlet-name>
<url-pattern>/pdf_nameoftheurl/*</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>mapfish.print3</servlet-name>
<servlet-class>org.mapfish.print.servlet.MapPrinterServlet</servlet-class>
<init-param>
<param-name>config</param-name>
<param-value>your_3rd_config_here.yaml</param-value>
</init-param>
</servlet>
<servlet-mapping>
<servlet-name>mapfish.print3</servlet-name>
<url-pattern>/pdf_anotherurlname/*</url-pattern>
</servlet-mapping>
I hope this gives you enough information to get it working!