I have created a copy of one of the main system apps(android system.apk) in which i have replaced some files to improve graphical view of my phone. is there any way to replace the two files or any other way to make changes directly to the application installed? any advise will be appreciated.
You can copy the new apk file directly on the folder where the old apk is located. I advise to copy it via recovery. If both apks have the same name, just replace the old one. If not, rename the new apk to have the same name as the old then replace it.
When you finish will need to clear the cache to avoid mixing up the old data with the new.
Important: Before processing with the copy/change operation, Do a backup of the old folder. It will be helpful to restore the old apk if things go wrong.