Yes, you need to rollover the SEP funds to a qualified plan in order to avoid "spreading" the conversion across your SEP plan and the non-deductible IRA basis.  This is critical to the backdoor Roth conversion strategy.

The IRS allows you to combine money in a SEP IRA with money in a 401(k) plan, either by moving the SEP IRA money to the 401(k) or the 401(k) money to the SEP IRA. Since both accounts offer pre-tax savings, you won't pay any taxes when you move the money.

However all of it is taxable if you do a ROTH conversion... it is not a "back door" event in any way.  So if you want to convert from the Sep to the Roth directly the tax liability is exactly the same as a SEP to 401K to Roth path.