"Does it mean though that if I would convert my SEP IRA to Roth now there would be less tax to pay than before this backdoor conversion?"
No, you would pay less (or at least have less taxable income) on future conversions because your traditional IRAs, including the SEP-IRA retain the portion of your basis in nondeductible traditional IRA contributions that are not applied to your Roth conversion.
"Does my backdoor Roth conversion increase my traditional IRA basis by $6000?"
No. The issue is that not all of your basis can be applied to your Roth conversion because you have other money in traditional IRAs (the SEP-IRA). For example, if your SEP-IRA balance is $94,000 and you make a nondeductible contribution of $6,000 to new traditional IRA account, then convert $6,000, only 6%, $360 of your $6,000 basis in nondeductible contributions is applied to the Roth conversion to make $360 of the conversion nontaxable, while the other $5,640 remains with your traditional IRAs to reduce the taxable amount of future distributions. If your SEP-IRA balance remains at $94,000, you make no other traditional IRA contributions and you convert the entire $94,000 to Roth, $5,640 of that Roth conversion will be nontaxable, consuming the remainder of your basis.
Review Form 8606 Part to see how the taxable amount is determined. Remember, for the purpose of determining the taxable amount of a traditional IRA distribution, all of your traditional IRAs are treated as if they are a single account.
