This sounds a little bit wrong. Because the kernel you downloaded and extracted will not be used. It doesn’t matter if it is there, so it is not really wrong but unnecessary.
Just create a folder, put all files form the Gitlab page in there (or just do a git clone) and edit all files you want to change. For example the PKGBUILD file if you don’t want all the Manjaro patches or change the config.x86_64 if you want a diffrent config for a x86_64 Kernel. Then run updpkgsums and makepkg with the appropriate options, for example
The makepkg will download, extract, patch and then build the Kernel, with the -i option also install. There is no reason for you to manually download and extract the Kernel.