Hi Lollipops,
other posters can probably give you more detailed info about the RER, but I have a few tips based on experience of a first visit to Eiffel Tower (and Paris), during first trip to DLP with my son last October.
I was really worried about doing this trip alone (discounting an oblivious tweenage son) with my haulting french and inexperience, but it was absolutely brilliant, definitely worth seeing, and we now have treasured memories and photos.
Tip one from me is to buy your train/metro tickets at one of the windows at Disney's station. They all seemed to speak English and you can have a conversation about where to get on/off trains, simplest ticket arrangements etc. It may be quicker to buy tickets at the machines but you don't get advice about the nearest toilets and taxis!
I found the RER incredibly easy to navigate - and it was my first time, with little french, and little experience of any underground at all! Electronic and plain signage at all the stations was very clear, and the couple of times that I wanted confirmation I found english speakers in the ticket windows again. Tip two for me would be to go armed with an RER map (tube map) and a Paris road/walking map, to help you feel in control.
On trains we found spaces for prams/wheelchairs, just like here on buses with the drop-down seats arrangements. Don't know if that's on all trains.
Tip three for me would be pick your times on the RER. I was told to avoid travel to Paris on a Saturday, it'll be crazy busy, and I've heard that Fridays are very busy too. Don't go too early because you'll get caught up in commuter rush, and leave Paris by 3.30pm latest to avoid the afternoon home time rush. We did catch this rush once on our trip and it isn't pleasant for kids.
Unless you're wanting to see other sights/attractions, I'd aim for an RER station within walking distance of the tower, but if you do need to travel by taxi they're everywhere there's an attraction, including tuk tuk taxis which we used and absolutely loved!
We went on a Thursday late morning and the queue for the lift entrance for the tower was about an hour. The stairs entrance queue was non-existant so we picked that one (cheaper too). Climbing up was OK but coming down did days worth of damage to my calf muscles! Sounds like you won't have this option if you have a pram, so I'd suggest making straight for the Tower in the morning (we took in some other sights first) to beat queues.
There is loads to see in the Tower area, lots of cheaper and gentler snack options just across the bridge in the Trocadero area (it's very busy directly under the tower itself), including restful gardens and the most stunning views of the tower. We took bottled water and a few snacks in case of getting stuck in hot queues and were glad of them, but there were some very fine ice cream and coffee options around!
I heard that pickpockets can be a problem on the RER and we took basic precautions, and there were buskers on the train - who were perfectly polite about being given a smile instead of a coin! We had no bad experiences on the RER and thoroughly enjoyed the journeys.
Hope you have a fantastic trip and an enjoyable day at the Tower.
