I can't answer any of your questions about API funds, but I can tell you something about transfers from a SIMPLE to an IRA at another custodian, if you decide to go that route.
After at least two years in your plan (you say you have 3, so you're covered) you can transfer all or any portion of your SIMPLE holdings to a Rollover IRA at the custodian of your choice (Vanguard, Fidelity, etc.) Depending on the rules of your present custodian and wherever you're moving it, this can be accomplished by liquidating/selling your old holdings, then transferring the cash in a custodian-to-custodian transfer. Once th funds show up in the Rollover IRA, you can reinvest the money in low-cost index funds, ETFs, or whatever you want.
It may also be possible to do an in-kind transfer, which moves the actual holdings from one custodian to another. I recently did this by moving individual equity holdings from my Fidelity SIMPLE to a Vanguard Rollover IRA, where I sold some and retained others.
You will want to ensure that your SIMPLE account remains open and active, so it can continue to receive employee contributions and employer matches. Pick the best investment offered by the plan (under the circumstances) and put the money there. I seem to recall reading something recently that implies a once-per-year limit for transferring additional funds; I don't recall whether this is a Vanguard rule, or an IRS rule. Anyone planning this should independently confirm any limits on making additional transfers. In my case, I kept a couple of Fidelity bond funds where new contributions are being invested.
If you really are paying 2%-plus you may want to just let contributions pile up in the money market or sweep accout until you can move them out of there (if that's an option).
To answer your concern about the boss finding out: No part of the process involves your employer in any way, shape or form. The transfer is completely between you, your old SIMPLE custodian, and your new IRA custodian. Because you are leaving your SIMPLE open to receive new deposits, your employer will continue making employee and employer match deposits as always.