You can provision your site through either Central Administration or PowerShell (if you have a lot sometimes it makes more sense to script them).
Since you're talking about upgrading, I'm assuming you're currently on SharePoint 2010, but your post isn't clear there. From a design perspective, you need to really think about what your plans are. Much like when we upgraded 2007 to 2010, upgrading 2010 to 2013 will result in some design rework if you want the 2013 look and feel. You certainly could upgrade to 2013 and keep the old 2010 ribbon instead of the 2013 look, but typically if you're going to upgrade you want to take advantage of all of the capability. It likely makes more sense to focus on designing a 2013 masterpage to deploy to your newly upgraded farm, rather than design something for 2010 and trying to upgrade it.
While it's possible to modify your masterpages and page layouts in SharePoint Designer, that is definitely not a best practice from either an implementation or maintainability perspective. The best practice approach is to develop your custom masterpages and page layouts, package them into a Visual Studio solution, and deploy that solution to your farm.