It's going to take time. Took you how long to learn ten fingers?
And yes, I'd recommend a separate sustain pedal. Put that where your right foot rests, put the EC5 where your left foot rests. Most of the switches in multi-switch units aren't designed for the same continuous usage that sustain pedals get, and also are placed higher up from the floor, making resting your heel on the floor and operating the switch more difficult.
I still feel 5 switches ain't enough. Once you get used to using your feet for Variation changes (with auto fill), that's going to tie up 4. Then Chord Sequencer's 2 (far better than the double button press the front panel makes you endure) and VH on/off (and you probably will need that a bunch) and even 7 get tied up quickly.
Just think... most organists had NO problem, with a bit of practice, running 12-24 'switches' to play basslines. Getting used to hitting a mere 5 occasionally will be a doddle.
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An arranger is just a tool. What matters is what you build with it..!