*Update (2-11-11)
Thanks to Sampsa Sohlman I was able to use the below code to display webcontent on each page in the theme.
init_custom.vm
#set ($header-content-id = "17302")
#set ($header-template-id = "NAV-RIGHT")
#set ($footer-content-id = "17403")
#set($header-content=$journalContentUtil.getContent($group_id, $header-content-id,$header-template-id,"$locale",$theme_display));
#set($footer-content=$journalContentUtil.getContent($group_id, $footer-content-id,null,"$locale",$theme_display));
portal_normal.vm
<div class="navigation-right">
$header-content
</div>
<div id="footer">
$footer-content
</div>
How to Embed Web Content within a Theme
The Client needed to be able to edit webcontent that would appear on multiple pages, in places that don't fit the regular layout template. The benifit of doing this, is that the user can update the web content, instead of the developer changing in the velocity templates each time and have to redeploy the theme.
Header Give Now Web Content
Footer Web Content

Step 1 - Create Web Content and make note of the Web Content ID.

Step 2 - Set the below code in your theme's init_custom.vm file.
The Web Content ID's don't match in my LOCAL, DEV, and PROD environments. So I set all of the Web Content ID's for each environment and then just uncomment the one that I am deploying. Also make sure to define "YOUR_COMMUNITY_NAME" and set the webcontent ID for each Environment.
If you plan on doing this for several themes make sure to set the 56_INSTANCE_HEAD to be unique such as 56_INSTANCE_HEAD2 or otherwise the content from the other theme might display on the theme you don't want it to.
init_custom.vm
## Configure Web Content
#set ($footer-instance = "56_INSTANCE_F00T")
#set ($header-instance = "56_INSTANCE_HEAD")
## Local Host
##set ($header-content = "17302")
##set ($footer-content = "17403")
## Dev
##set ($header-content = "13620")
##set ($footer-content = "13590")
## Prod
#set ($footer-content = "13503")
#set ($header-content = "13737")
## #* Service Rational *# ##
#set ($layoutLocalService = $serviceLocator.findService("com.liferay.portal.service.LayoutLocalService"))
#set ($groupLocalService = $serviceLocator.findService("com.liferay.portal.service.GroupLocalService"))
#set ($userLocalService = $serviceLocator.findService("com.liferay.portal.service.UserLocalService"))
#set ($roleLocalService = $serviceLocator.findService("com.liferay.portal.service.RoleLocalService"))
#set ($usrgrproleLocalService = $serviceLocator.findService("com.liferay.portal.service.UserGroupRoleLocalService"))
#set ($grp = $groupLocalService.getGroup($theme_display.getPortletGroupId()))
#set ($user2 = $userLocalService.getUserById($grp.getClassPK()))
#set ($guestGroup = $groupLocalService.getGroup($company_id, "YOUR_COMMUNITY_NAME"))
#set ($journalArticleLocalService = $serviceLocator.findService("com.liferay.portlet.journal.service.JournalArticleLocalService"))
#set ($portalgroup_id = $group_id)
#set ($portalguest_id = $guestGroup.getGroupId())
Step 3 - Place the corresponding code within your theme template file.
I added these web content items in my portal_normal.vm but you can place them in what ever theme template file you want the content to show up in. I left the div and class name to wrap the webcontent so that it gives more information what that peice of web content is, instead of just the variable of $header-content
portal_normal.vm
<div class="navigation-right">
#if ($journalArticleLocalService.hasArticle($guestGroup.getGroupId(), $header-content))
$velocityPortletPreferences.setValue("portlet-setup-show-borders", "false")
$velocityPortletPreferences.setValue("group-id", "$guestGroup.getGroupId()")
$velocityPortletPreferences.setValue("article-id", $header-content)
$theme.runtime("$header-instance", "", $velocityPortletPreferences.toString())
$velocityPortletPreferences.reset()
#end
</div>
<div id="footer">
#if ($journalArticleLocalService.hasArticle($guestGroup.getGroupId(), $footer-content))
$velocityPortletPreferences.setValue("portlet-setup-show-borders", "false")
$velocityPortletPreferences.setValue("group-id", "$guestGroup.getGroupId()")
$velocityPortletPreferences.setValue("article-id", $footer-content)
$theme.runtime("$footer-instance", "", $velocityPortletPreferences.toString())
$velocityPortletPreferences.reset()
#end
</div>
*Disclaimer I'm a front-end prgrammer so I don't know what each line of the velocity code does, but I mainly just worked with changing the bolded and underlined items