"I presume the brokerage must keep track of which contributions are mine and which are from my employer when determining basis"
All of the employee and employer contributions made to a SIMPLE IRA are pre-tax. Your employee elective deferrals, the employer contribution and any investment earnings in the SIMPLE IRA do not result in any increase in your basis in nondeductible traditional IRA contributions.
Even if you do have basis in nondeductible traditional IRA contributions derived from other sources, IRA custodians have no way to know how much basis you have because they don't file your tax return (which is what establishes such basis). It's your own responsibility to track any such basis so that you can correctly prepare Form 8606 when you receive an ordinary distribution from any of your traditional IRAs, including the SIMPLE IRA.
IRA contribution entries under Deductions & Credits are only for deposits that you personally make to an IRA, not for any made to employer plans.
