If you want to use sand, make sure it is fine silica based sand and I would wait until the axolotls are bigger than 5 inches long. Smaller axolotls cannot pass sand through their system safely so it is not recommended to use sand when they are smaller than 5 inches.
Some people say axolotls have trouble gripping the bottom with bare bottom. Others say it is not an issue. I think it is down to personal choice. Personally, I prefer substrate over bare bottom. I think it looks nicer and I got the feeling my axolotls prefer the sand. I use play sand and quite like it. As Lucyz83 mentioned, I also had issues with aquarium sand I purchased. I didn't realise how coarse it actually was and had issues with one of my axolotl's ingesting some. The play sand is much finer and I have not had any issues since.
I would not use large river rocks as you need to ensure they are big enough not to be swallowed (bigger than the axolotl's head) and debris can easily get trapped between the rocks and it is harder to keep clean.
Whatever you use, it is up to you and personal preference. Just be sure that if you use sand, to wait until your axolotls are bigger than 5 inches and if using big rocks be sure they are bigger than your axolotl's head to ensure they cannot be swallowed.