Jim,
1. Patio - I assume this is a paver patio. If so there should have been at least 4 inches of compacted aggregate as a base, then 1 inch of sand and then the pavers. A polymeric sand or something like sand with glue mixed in should have been used to fill in the joints. If this was all done correctly you should rarely see a weed. To kill and prevent further weeds do not pull them.. spray them with a mixture of roundup and pre-emergence.
2. Pond/waterfall. The thick pond liner should be under the rocks, then it should not leak. The rocks themselves should not be a part of the leak/noleak equation.
3. Unsolicited advice... It sounds to me like your poor choices are part of the problem. Going through two landscapers and then trying to finish it yourself is an indication you initially took the low bidders. Hiring a quality company, paying a reasonable price, and then letting them alone while they do their work... is the best way to not have regrets.