Applying for NEXUS is treated by CBP and CBSA as a brand new process. Nobody will care that you are GE - the process is the process, and it is a LOT slower than GE (supposedly because the CBSA can't process applications as quickly as CBP).
I did GE, then NEXUS, mostly because it was easier to start with GE and get PreCheck benefits immediately. I don't travel to Canada more than once or twice per quarter. At the time when I was GE-only I was also mostly crossing at Thousand Islands in the winter, which meant I didn't have much in the way of lines going in to Canada and I could use my GE card in the NEXUS lane entering the US.
The main benefit of NEXUS over GE is expedited ENTRY to Canada, which you don't get from GE. If you fly in or use a busy land crossing but only have GE, you get to wait in the standard line on the way in to Canada. You can still use GE on the way in to the US (either with the card at a land crossing NEXUS lane, or with your passport and fingerprint biometrics when entering the US or using the Preclearance facilities at major Canadian airports.)