I run my tanks without a cap. Tends to get mixed, and no way to separate it. It won't keep the plants down any better.
To rinse or not is up to you. An easier way is to dump it into the tank and deliberately make a mess, stirring and then drain. Repeat. When you have done this a couple of times be much more careful not to make any more mess, and set up the 'scape. Rinsing the substrate in the tank is much easier than in small buckets.
When you fill the tank put a plate or plastic bag over the substrate and pour the water in slowly so it seeps over the edge of the bag and into the substrate.