Hi, Bill.
John has given you good "how to" advice. But you might also need some "whether to" counseling, although you didn't ask for it.
Many organizations, especially non-profits, are required to keep certain funds strictly separate and to NOT commingle them. As just one example, a church member may have donated a sum of money to be used only to fund an annual church picnic. Even if there are tons of excess cash in that fund, it may not be legally available to pay the church's utility bills.
Also, many organizations are divided into separate sub-organizations for management or other purposes. One sub might own the church building, for example, and rent it to one or more subs; to those other subs, the rent check is not just a transfer, but an expense. There may be a mortgage with legal requirements for segregating the funds.
The key part of your question is your parenthetical,"(for some reason which I cannot understand)". Please don't change the system UNTIL you understand WHY it is being done this way. It may be, as you suspect, simply some prior treasurer's whim. But it may be based on solid legal or management considerations.
If you search the archives here, you will find my prior treatises on why Quicken should not be used for what I called "third-party accounting". It is a fine product for keeping my own records for my own (first-party) purposes. It is not too bad for second-party accounting, such as for my minor children or elderly aunt, or for preparing my own income taxes or applying for a personal loan at my bank. Quicken is only a tool to organize the information that I'm submitting to the IRS or bank; they are relying on my representations and don't care if I used a computer or a pencil to arrive at those numbers. But for a situation where you will need to submit reports to unrelated parties (your church board and members, for example), you really need an accounting system that is auditable. Quicken allows any entry to be changed or deleted with no trace of who deleted it or why - or even that it was deleted. That kind of system is simply not suitable for accounting that will be relied on by third parties who did not actually keep the books. That is my professional opinion. I urge you to consult with someone you trust who is knowledgeable about matters, perhaps a CPA or attorney who is a member of your church. Not about "how to", but "whether to" use a different accounting method.
RC