First, to answer your question, I believe the safest way to pay is through a money order but you must keep the receipt so that you can prove payment. I do not advocate paying by check because they may hit your account again once they have the routing numbers and other information (same is true for credit cards).
I assume that you have a deal with teh collection agency as to what the terms of payment will be. I strongly urge you to get something in writing from the collection agency as what the terms of payment are. I would not accept anything they say over the phone. Get it in writing. You also want them to confirm that they have authority from the original creditor to make a deal with you.
Finally, a word about debt buyers. There are entities that purchase portfolios of charged off credit card accounts. They will sue you but a lot of times, you can beat them in court. As an alternative, they will often make deals with you at substantially less than what is owed.
Do not trust the collection agencies. Get it in writing and do not every give anyone access to your checking account.
By answering this question, general information is provided and no attorney-client relationship is established. For specific inquiries, you should consult with experienced counsel in your area.
I am not convinced that it matters one way or another how you pay as long as you can provide documentation that the payment was made.
It sounds like you are worried that if you use a check or a credit card that the creditor could take money in the future without authorization. Talk to your bank about this, but I don't see this being a serious risk. If the creditor takes funds without authorization, you can dispute it and if the creditor pulls this kind of stunt very often, they will lost their right to accept credit cards and their bank will shut down their account.
Keep a paper trail of every communication, payment, and all terms. As a condition of settlement, confirm that the payment is settlement in full and satisfaction of any obligation for that debt. If a suit is pending, demand a withdrawal of suit with prejudice and ask creditor for general release if possible.