I assume that

company -> settings -> customer&sales -> linked accounts

the bank account to use is '1020 cash to be deposited' (ctbd)

when you recorded the payment,the transaction is

1020 ctbd   $100 db

1200 ar        $100 cr

now when you use banking -> make deposit

the account is 1060 chequing bank account

and you select the cheque(s)

the transaction is

1060 bank acct  $100 db

1020 ctbd          $100 cr

sounds like your linked acct is the default, ie. bank acct

Yes, I recorded the deposit using 1020, and the account when I reconcile  is 1060. So how do I go about correcting this? I can't find a path, and the deposit doesn't allow me to void or delete and start over.

there's an article that describes how to deal with this situation (because you can't void/delete a deposit)

this post has a link to it, ie. "here"

sagecity.na.sage.com/.../71683.aspx

Okay, I will fix the deposit this way. If I want to use deposit slips, is the correction jut to make sure I use acciount 1060, and then it will show up as just a deposit when I reconcile? I prefer to use deposit slips because I has so many deposits, that it helps manage the deposits over the course of the month into manageable bits, as opposed to trying to find all the monthly deposits in the reconciliation without making a mistake that is then hard to find due to the number of deposits I receive.

Hmmm, when I went to reverse the receipt as recommended in the link you sent, there is no line for that in the receipts drop down. ??