Does an employee who has a SEP or SIMPLE IRA contact their employer to initiate a distribution, or do they contact the financial institution where the account is held?

The employee is the account owner of the SEP or SIMPLE IRA and initiates a distribution from their IRA with the financial institution that their account is held at.

The employee is the account owner of the SEP or SIMPLE IRA that is held at a financial institution. The employer establishes the plan, agreeing to provide benefits to all eligible employees by contributing to an employee’s traditional individual retirement account or annuity (traditional IRA) or SIMPLE IRA. They make contributions directly to an IRA set up by or for each employee with a bank, insurance company, or other qualified financial institution. 

All amounts contributed to an employee's IRA by an employer belong to the employee, even after contributions stop. Distributions from the IRA are initiated by the employee (account owner) at the financial institution in which the funds are held at.  Outside of depositing to a SEP or SIMPLE IRA for an employee, the employer cannot initiate or complete transactions from an employee's SEP or SIMPLE IRA or make investment decisions.

For more information refer to IRS.gov. 

https://www.irs.gov/retirement-plans/plan-sponsor/types-of-retirement-plans