This account has done nothing but cause problems. Half of the time we have to force it to apply, and when you have over 2500 clients, to look at each one is stupid. My old software would immediately apply and it would show in the control. Why can't this? Is there a rational reason why we have to have this go to unapplied first?

You can set a Business Rule to automatically apply new payments.  From the Configuration page, click Business Rules, Highlight the General option, Select Always from the Automatically apply new payments and Automatically apply new credits drop-down menus.  This can also be client specific by defining this setup on the Defaults Tab of the Client Record.  I hope this helps!

Heather's right about the automatic application.  You can check the box to automatically apply payments and credits.  However, the question about multiple AR accounts is a separate one.  You need to have an unapplied payment account if you track you receivables through multiple accounts.  This way if you receive a payment and there is no charge to apply, you can have it in a holding account until the charge comes in (then you apply and the system creates the journal entries to move it out of the unapplied and into the AR account that is defined on the charge).  

If you are in multiple AR accounts and you do have an open charge when you add a payment, the system will automatically replace the holding account with AR at the moment you apply.  It seems the decision was made to go with multiple Accounts Receivable accounts in your system.  So I'd check to see why that may be.  Single AR setup is easier to reconcile and simpler for applications (no holding account), but multiple allows you more flexibility and also granularity on your balance sheet.