Sounds like you are getting confused with your RA axis, on a dob the "RA" axis is the base board centre, or the right / left slewing motion. Your Dec axis is your up / down motion.
To have it polar aligned (which as Gary pointed out is nonsensical) you must tilt the base board so the centre-line of the bolt used to hold the base together is pointing to the SCP, not the tube! But doing this is not in the design of the Dobsonian mount, it is purely an Alt/ Azimuth mount.
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