To make updates in game you have to open the SMC -> Go to ModulePatch -> Right Click SR_Client (Patch : SR_Client 22 will pop up, click on it) -> Read Patch Data -> Analyze Patch Data -> Start Upload
But you have to make sure that you have the files you want to update in Patch_Internal (SMC Folder)
as for the logo, you can extract logo.ddj, logo-big.ddj from Media.pk2 (Media.pk2 -> Interface -> outer) and use

to convert the files to png, make sure to get the photoshop dds plugin in order save it and to avoid any issues (Since you can't save png to ddj directly) you'll have to use dds to ddj/ddj to dds -download from the attachment.
Edit: Let's say for example you want to update the logos.. you'll copy the interface folder which contains your outer (folder) changes and paste it on Patch_Internal and make sure to create a folder named media or data or whatever the .pk2 you want to update is (without capital characters) pretty much like the path of the extraction but the difference is, instead of "Media", you'll rename it to "media"