For each print (including your first), I’d recommend using the appropriate tool head for the filament. The original head should be used for PLA, ABS, PETG, and any other “hard” filament types. The Flexytruder should be used for Ninjaflex and any other flexible filaments.
When you switch tool heads, you will also need to switch the firmware. Before switching, use the LCD panel or CuraLE’s Monitor (with the printer connected) to determine the current E-steps (under Manual control, select Console and enter M503 and look for the M92 line) and the current Z-offset (enter M851). Write these down and keep them with the tool head.
Both tool heads may have a sticker on them (usually on the back) that has the E-steps value for that head. I put a sticker on the front with the E-steps and Z-offset because I always forget to look at the value on the back before I mount the tool head I’m about to use.
You should have two printers defined in CuraLE, When you switch tool heads (printers) in CuraLE, you will have the option to upgrade the firmware.