While for some this may seem trivial i know there will be others that are unaware of how simple it is to update your phpMyAdmin installation.
Currently, at the time of writing this, the latest version released by Synology is 3.5.3-0003 and the current version of phpMyAdmin is 4.1.1.
To update your installation you simply need to download the latest version from phpMyAdmin.net and extract the .zip file to a convenient place like your desktop. once that is done you need to connect to your Synology NAS and navigate to the ‘Web’ folder. This can be done a number of ways but i will show you one in particular, now, i am a mac user and hence i will demonstrate using OS X.
First click on the ‘Go’ menu from the top MenuBar
Once you have done so you will be prompted for your Synology NAS details. You and either enter in the IP of your NAS, if you know it, or you can simply enter the hostname (what you called your NAS).
You will then be prompted to logon to the NAS
Once you have entered your credentials and successfully logged in, you will be asked which of the shared folders you would like to connect to (this will be shown as a network drive on your desktop).
You want to select the ‘Web’ folder from the list of available shared folders. There will be a folder called phpMyAdmin within your Web folder, this is the one you want.
This is the important part. The file config.inc.php needs to be kept intact, you DO NOT want to overwrite this file. Copy it somewhere safe, back it up, the choice is yours.
Now all you need to do is copy the contents of the .zip file you previously downloaded and extracted to your desktop into the phpMyAdmin folder you have open on your NAS remembering not to overwrite the config.inc.php file.
Once you have done all of the above you simple need to stop/start the phpMyAdmin service on your Synology NAS. The easiest way is from the Package Manager.