Concerns about trial separation and how it affects my rights for child custody

Need some advice here. I want to say that I love my wife with all of my heart and have been married for 6 years. Recently, we have been going through a rough patch and in her words "have grown apart", "I love you, but not in love with you" and "its not you, I (wife) has changed". So we agreed on a trial separation as a last chance to see if she wants to continue with the marriage. The marriage counselor agreed with this as long as we were both in agreement with this. At this point, I will try anything and honestly believe that if I can show her my love for her by letting her go, then maybe she will see it and come back to us. The question that I have, is that in this trial separation, she is going to take our son to live with her. She agreed to move out, rent a place and only take the things that she came into my house with and some other small agreed upon items (some pots, kitchen items, etc ...). In the agreement, I will continue paying for the car insurance, health insurance through my job, our 3 year old son's day care and give her a monthly payment for "child support" as she put it. We are quickly deciding on the amount right now. We also agreed on a 50/50 plan for our son, meaning that every two days he will stay over one of the parents house with alternating weekends at each parents house. On the evening of when our son goes to the other house, we will all have dinner together. This will help show our son that we are civil and might help with the communication between us. So the million dollar question that I have, is if we go through with this and I pay the perceived "child support" and I really digging a hole for myself if we decide to get a divorce? Am I setting a precedent that automatically gives her custody of our son. Thank you and I really do not just want to hand over custody of our child. I want to do the right thing and will do so if that truly is the best for our son, but I just don't want to give him up because a precedent was already set from the trial separation. Any advice about this or about any part of my situation?

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