A few years late, but to all those trying to do this in 2018:
<block class="Magento\Framework\View\Element\Template" name="linkboxes" template="Magento_Theme::phtmlfileyouwant.phtml" after="logo"/>
I find if you just want a Magento CMS block, try something like below inside the PHTML file.
<?php echo $block->getLayout()->createBlock('Magento\Cms\Block\Block')->setBlockId('[BLOCK ID]')->toHtml() ?>
However I generally don't reference a CMS block I just put whatever I'd put in the block in the PHTML file. I find this gives me more control over what I'm doing, (for instance allowing me to insert my own PHP script checking for cookies when the PHTML file loads, allowing me to then alter what my PHTML says as a result of the cookie check)