It will still work. You hit record, change a parameter and after that check which CC# or polypresure note that has changed (in Cubase this is in the controler lane). If i remember right the arp parameters are controled by polypressure messages but can also send as sysex so if your controler supports this it can be done.
You could also, if you find it easier, assign arp on/off (actually it´s "arp mode" you want to control, 0=off, 1= up, 2=down, etc.) or another parameter to a known controller (the modwheel, breath or whatever) in the mod matrix and just set your controler to the same parameter. Only downside with this aproach is that you have to do this with all the pathces you want to control...
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