Nothing about the SEP IRA prevents you from making a QCD from the regular traditional IRA. As long as you have at least $1,000 of pre-tax money in all of your traditional IRAs, you can make a $1,000 QCD from the regular traditional IRA. You just can't make a QCD from the SEP IRA since it's an ongoing SEP IRA. (Nothing prevents you from doing a trustee-to-trustee transfer of funds from the SEP IRA to the regular traditional IRA to be able to make a QCD from the regular traditional IRA.)
When you are over age 70½ and enter a Form 1099-R that has code 7 in box 7 and the IRA/SEP/SIMPLE box marked, TurboTax will ask if you had any of the distribution transferred to charity and, if so, the amount transferred to charity. TurboTax will include this amount on Form 1040 line 4a but exclude it from the amount on line 4b with the "QCD" notation next to this line.
