Plelase install commerce r2sp2 into deployment center on machine you will be updating source control

C:\Program Files (x86)\EPiServer\CMS\6.1.379.0\Install\Modules\EPiServer Commerce 1.1.2.62\MediachaseECF

Extract the zip file somewhere ex C:\Temp\EPiCommerce

Extract the zip file in C:\Temp\EPiCommerce\Data\DeploymentPackage.zip to C:\Temp\EPiCommerce\DeploymentPackage

1. Database upgrade run C:\Temp\EPiCommerce\DeploymentPackage\SqlScripts\Helpers\Update-Main.bat from command prompt with paramters usernmae password database server
2. Shared Files Directory you will need to update the shared/apps folder with the apps folder from C:\Temp\EPiCommerce\Mediachase\eCommerceFramework\5.2\Shared\Apps\
3. Resources and bin 
1. Copy C:\Temp\EPiCommerce\DeploymentPackage\B2CSampleSite\App_GlobalResources\ to your commerce site root and your cms site root.
2. Copy C:\Program Files (x86)\EPiServer\CMS\6.1.379.0\Install\Modules\EPiServer Commerce 1.1.2.62\bin to commerce site bin and cms site bin

That should be all of the things you need to do.  I would not advise upgrading the cms website files if you have already started to chnage the controls.  You could always download the sample and see if there are any new files or chnages but I would think it is not really neccessary.