A regular nondeductible traditional IRA contribution for 2015 should have been reported on your 2015 tax return and your 2015 tax return should have included Form 8606 with the contribution being included on line 14 for carrying forward to line 2 of your 2016 Form 8606.
In 2016 TurboTax, be sure to click the Continue button on the Your 1099-R Entries page, indicate that you made nondeductible traditional IRA contributions, then enter or confirm the amount that carried forward from line 14 of your 2015 Form 8606. The taxable amount of your 2016 Roth conversion will be calculated on the lines that follow, or perhaps on a separate worksheet, indicated by an asterisk. If your IRA accounts, including your SEP IRA account, had a nonzero balance on December 31, 2016, at lease some of your 2016 Roth conversion will be taxable, perhaps a large amount depending on that year-end balance.
You said that you contributed your spouse's IRA contribution to your IRA account. I hope that's not what you meant to say. Your spouse's contribution must be made to your spouse's own IRA account, not you your account. IRAs are individual accounts and each individual carries their own separate basis in nondeductible traditional IRA contributions.
