The 90-day clock starts ticking the moment you enter Spain.The 90-day regulation is enforced across the whole Schengen countries, and not just in Spain.
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If you wish to be in Spain for longer than 90 days every 180, you must apply for a visa before you enter the country. There's a variety of visa options for both short and long-term stays. Read about long-term Spanish visas.
Once you leave, you cannot return to Spain (or Schengen) without a visa until a further 90 days have gone by. For example, if you have spent 90 days in total in Spain and leave on June 29th, you cannot go back without a visa until at least September 28th.
Retiring to Spain from the U.S.A. is perfectly possible. However, for stays of longer than 90 days, Americans need to get a visa to live in Spain. There is no Spain retiree visa, but there is a Spain long term visa known as a residence visa. There is also the Spain long stay visa called a “Golden Visa.”
Luckily, when you've applied for your TIE card and are waiting for it to arrive, you can leave Spain by applying for Autorización de Regreso, an authorisation to return.