Hi Dee Gladney,

Just modify \tpls\blocks\header.php.

You can move the content of the main navigation to the header.php block.

For example, we have did it on JA Argo: http://joomla25-templates.joomlart.com/ja_argo/

<!-- MAIN NAVIGATION -->

<nav id="t3-mainnav" class="wrap t3-mainnav navbar-fixed-top navbar-collapse-fixed-top">

  <div class="container navbar">

    <div class="navbar-inner">



      <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">

        <i class="icon-reorder"></i>

  	  </button>

      

      <!-- LOGO -->

      <div class="logo logo-<?php echo $logotype ?>">

        <h1>

          <a href="/<?php echo JURI::base(true) ?>" title="<?php echo strip_tags($sitename) ?>"<?php echo $logoimage ?>>

            <span><?php echo $sitename ?></span>

          </a>

          <small class="site-slogan hidden-phone"><?php echo $slogan ?></small>

        </h1>

      </div>

      <!-- //LOGO -->



      <div class="nav-collapse collapse<?php echo $this->getParam('navigation_collapse_showsub', 1) ? ' always-show' : '' ?>">

      <?php if ($this->getParam('navigation_type') == 'megamenu') : ?>

        <?php $this->megamenu($this->getParam('mm_type', 'mainmenu')) ?>

      <?php else : ?>

        <div class="mainnav-wrap <?php $this->_c('navhelper') ?>">

          <jdoc:include type="modules" name="mainnav" style="raw" />

        </div>

      <?php endif ?>

  		</div>

  		

  		<?php if($this->countModules('languageswitcherload')): ?>

  		<div class="languageswitcher">

  			<jdoc:include type="modules" name="<?php $this->_p('languageswitcherload') ?>" style="raw" />

  		</div>

  		<?php endif; ?>

  		

  		<?php if ($this->countModules('followus') || $this->countModules('login')) : ?>

  		<!-- USER, FOLLOW US -->

			<div class="head-social">

				<ul class="nav">

						<?php if($this->countModules('followus')): ?>

						<li class="dropdown parent nav-connect">

							<a data-toggle="dropdown" href="#" class=" dropdown-toggle">

								<i class="icon-plus"></i><?php echo JText::_('TPL_FOLLOWUS') ?>

							</a>

							<div class="nav-child dropdown-menu">

								<div class="dropdown-menu-inner">

									<jdoc:include type="modules" name="<?php $this->_p('followus') ?>" style="T3Xhtml" />

								</div>

							</div>

						</li>

						<?php endif; ?>

						<?php if($this->countModules('login')): ?>

            <?php $user = JFactory::getUser(); ?>

						<li class="dropdown parent nav-user<?php echo ((!$user->get('guest')) ? ' logged' : ''); ?>">

							<a data-toggle="dropdown" href="#" class=" dropdown-toggle">

								<i class="icon-user"></i>

                <?php echo ((!$user->get('guest')) ? '<span class="uname">' . $user->get('name') . '</span>' : JText::_('TPL_USER')); ?>

							</a>

							<div class="nav-child dropdown-menu">

								<div class="dropdown-menu-inner">

									<jdoc:include type="modules" name="<?php $this->_p('login') ?>" style="T3Xhtml" />

								</div>

							</div>

						</li>

						<?php endif; ?>

				</ul>

			</div>

			<!-- //USER, FOLLOW US -->

			<?php endif ?>

	

      <?php if ($this->countModules('head-search')) : ?>

      <!-- HEAD SEARCH -->   

      <div class="head-search">

        <jdoc:include type="modules" name="<?php $this->_p('head-search') ?>" style="raw" />

      </div>

      <!-- //HEAD SEARCH -->

      <?php endif ?>



    </div>

  </div>

</nav>

<!-- //MAIN NAVIGATION -->

We have the similar markup in JA Fixel: http://joomla25-templates.joomlart.com/ja_fixel/

You can download those two templates and check it as reference.

Regards