The credit you are refering to is the Child and Dependent Care Expense Credit that up to $3,000 per qualifying person per year can be claimed. What I'm saying is that no matter how much you spent, not a penny over $3,000 per qualifying person with a $6,000 max, no matter how many qualifying persons there may be, can be included. Then only a percentage of that is deducted from the taxpayers tax liability (20 to 35% depending on the Adjusted Gross Income of the taxpayer).
You can pay as much as you like towards your sons daycare, but it won't help you taxwise or hurt your son's father because you don't claim your son as your dependent. If you did and claimed the credit, the first $3,000 of your pre-tax dollars would be dissallowed and only the taxed monies spent would be considered.
Since you aren't eligible for this credit in the first place, you end up having to report these monies that were not taxed to your income at the end of the year and you get taxed on them anyway. It is most beneficial to let whoever is eligilbe take the credit, (your son's father since he claims the child) and pay the first $3,000 which is all that can be included in claiming the credit in the first place. After that, it is a mute point. Hope this answered your question. If not, feel free to email me with any questions.