OK, @ipaqrat, I promised in a personal message I would explain how this works in the USA. I’m posting my answer on the public forum because several of the non-USA members have made comments that could potentially mislead other readers. These nuances originate with fundamentally different approaches to taxation between jurisdiction.
First, you and your partners are using Expense Claims basically correctly. That is, you are posting expense claims to record the expenditure of personal funds for legitimate company purposes. When you do so, a liability is established because the LLC (a type of company for those not familiar with US terminology) owes money to the partner. You have the choice of reimbursing the partner from a cash or bank account, as you would if the claim were filed by a non-owner employee, or clearing the liability to the partner’s capital account. You’ve obviously chosen the second approach, and I agree that generally makes more sense than the first approach, since things all come out in the wash through your capital draws anyway.
Second, understand that because an expense claim is not a transaction into or out of company accounts. That transaction comes later, when the claim is settled. So the entire business of tax-inclusivity or -exclusivity as normally discussed by other Manager users is moot. The company is neither collecting nor paying tax of any kind on the expense claim.
Third, Manager’s tax-inclusive feature allows one to record transactions where tax is already included in the price. As you know, that is virtually never the case for sales tax in the US. (Typical exceptions are for de minimis purchases such as snacks at a concession stand, where, in some jurisdictions, vendors can quote a tax-inclusive price to simplify change-making.) So you will probably never use the tax-inclusive feature operating in Virginia.
So how do you handle these transactions? To answer that question, you must consider Internal Revenue Service (IRS) rules. Perhaps the most important one is that allowable expenses include applicable sales taxes, freight-in, and installation. For example, the purchase of a $100 item with 6% sales tax and a $15 shipping charge should be recorded as a $121 expense. This is true regardless of whether the purchase is a current year operating expense, a contributor to cost of goods sold, or a depreciable capital asset. (There are some details about expensing items under the de minims safe harbor rule that suggest getting separate invoices for freight-in and installation costs, but that’s another discussion.) So there is no need to record or break out the $100 item, the $6 tax, and the $15 shipping charge separately. Nor should the tax and shipping be charged to separate accounts from the item. That determination should depend solely on the classification appropriate for the purchased item itself. The tax and shipping are allowable expenses (and therefore deductible) if the item is allowable.
Understand the difference between sales tax paid on expensed purchases, business taxes paid, and sales taxes remittable to the state/county/city. The first I have discussed in the preceding paragraph. That sort of sales tax is lumped with the overall expense, so need not be broken out separately on the expense claim. Business taxes paid might include property taxes, inventory taxes, and so forth. They have nothing to do with expensed purchases. And, of course, sales taxes remittable are merely being collected by you on taxable sales and passed along to the taxing authorities. But since services are not taxable in Virginia, you probably collect these seldom, if ever.
You said that you frequently combined personal and business purchases on the same receipt. While that is legally acceptable to the IRS, it is poor practice, mostly because it is cumbersome. You must, in fact, prorate the sales tax to the items in order to allocate it properly. It would be better, even if purchasing things at the same store at the same time, to make two transaction so the receipts are clean. You might extend that philosophy to purchases that will eventually be allocated to different expense accounts, too, though there is no legal need. But again, you will have to prorate sales tax on the copy paper recorded to the Office Supplies account separately from that on packaging tape recorded to the Shipping Supplies account.
Returning to the clearing of expense claims, there is again no reason to worry about the sales tax components. Partner A charged $121 to her personal credit card when special-ordering the item discussed in my earlier example. That constitutes an equivalent contribution of capital, no matter what the company uses that capital for. So the entire amount can be cleared to Partner A’s capital account with a journal entry. No need to break out sales tax separately.
Now, you said in your original post that you allocated businesses expenses to appropriate accounts, “some taxable, some exempt.” I’m not sure what you meant. If an expense is allowable, it is deductible. If the item purchased is actually sales-tax-exempt, no sales tax appears on the receipt for that item. So there is no reason to consider sorting things into different accounts on that basis. Any situations where allowable expenses are not fully deductible (such as meals and entertainment expenses), are handled outside Manager on the tax forms. From an accounting perspective, they were still legitimate business expenses.
Hopefully this has helped. If you have other questions, please ask. And remember, I’m not an accountant, and I am definitely not providing tax or legal advice. I am merely attempting to explain how expense claims can be handled in Manager within the US tax environment. 
