I may not understand your question or the entire situation, but I have some thoughts.
As a US citizen, you are required to report and pay US tax on all your worldwide income, no matter where you are living at the time. If you live overseas more than 330 days of the year, you can claim the foreign earned income exclusion, which excludes foreign earned income from taxation. However, because you have structured your company so that most of the profits come to you as unearned income, you would not qualify for this exclusion.
The owner of a subchapter S corporation must pay themselves a fair market salary for their participation in the business, that is to say, a similar salary to what you would pay a stranger to do a similar level of work. If most of your income is passive, and you don’t participate very much, then it might be OK to take a salary that is less than 5% of the profit, but I think that would be unusual and I suspect your fair market salary should be much higher.
Your business is allowed to report ordinary and necessary expenses, regardless of where they are incurred. If you operate the business overseas and have expenses overseas, they are deductible against your business income. There is no reason not to take the deduction.
As stated, by @Critter-3 , as a W-2 employee, you are not allowed to deduct home office expenses. Your company can reimburse you tax free for legitimate expenses if you use an accountable reimbursement plan, but you would have to have very good records to show the reimbursable cost of the home office.
