Having now used the Expense Claims module quite a bit and done some experimenting, I believe I can explain some of what you are seeing.
You are correct that expense payers are not linked in any way to employees. However, they may be linked indirectly to owners, depending on your form of organization and chart of accounts.
First of all, understand that Expense Claims are used to record payment of company expenses with non-company funds. Examples are travel expenses that will eventually be reimbursed to the traveler or mileage expenses that are deductible for tax purposes but may never actually be reimbursed (such as when a sole proprietor drives a personal vehicle on company business.
When entering a new expense claim, you must record the expense as being paid by a defined payer. Payers might be employees, partners, or proprietors. If they are employees, you will need to first set them up as payers. If they are partners or proprietors, you may set them up as payers, but you also have other choices. Manager includes all defined payers in the payer drop-down menu. But it also includes members for whom capital accounts have been defined. If you define a name as a payer for which there is already a capital accounts, you will see that name listed twice, which could be confusing and should thus be avoided.
My personal recommendations are as follows:
For employees, create a payer. Record out of pocket expenses against the account of that payer. Then periodically reimburse from a company account. You might put that on a payslip or create a separate transaction, either as a journal entry or by using the spend money feature.
For partners, you should already have created capital accounts. So do not define payers. Simply enter expense claims against the appropriate partner. Their equity in the company will automatically be adjusted, since an unreimbursed payment of a company expense is financially equivalent to an additional contribution of capital. If you want to be old fashioned, you could reimburse via a drawing account and then close the drawing account at the end of the year, but Manager really makes it unnecessary to close (or in many cases even to have) such temporary accounts. You just define report and Summary periods by the desired accounting interval so the displayed balances do not grow endlessly.
For a proprietorship, define a payer and periodically close the expense claims to whatever you call your owner equity account. Until you do that, the claim will be carried as a liability. You need not define the owner as a member, since the single owner’s and company’s equity positions are the same thing. How often you need to close expense claims to owner equity depends on how current you want the summary to be. Of course, you could also create a member capital account for the single owner and handle expenses claims just as outlined above for partners, but that ends up requiring a few more steps.
If you use an outside accountant, he or she may want to impose other preferences. The great thing about Manager is that you can be more or less traditional in terms of temporary accounts, summary accounts, and period-ending closings. In my own case of a sole proprietorship, I’ve realized I can completely avoid several steps in the classic accounting cycle, yet still produce exactly the same reports and have the same visibility into my equity position and performance. If I wanted to apply for a loan, for example, I could produce exactly the same financial statements and reports bankers have been looking at for centuries. But it would have been much easier for me. That’s the beauty of Manager, in my opinion.