The peppers will pollinate themselves without any assistance if you give them the conditions they want in order to be fertile. Taking a small paint brush or cotton swab can help, as can shaking the plant or putting a fan on it, but getting them producing viable pollen and receptive to it is the key. What you're looking for is the split in the anthers that opens and starts to produce visible/fuzzy pollen. Lots of it, not just a little. That's when it's time to expect sets and to hand pollinate. Usually this happens within a couple hours of lights on once flowers develop and the environment is right.
For rocotos, you may wish to create a day/nigh temperature differential of at least 10 degrees. Some people spray the plants each night with cold water to trigger them if conditions are such that it stays warm at night. Rocotos don't produce their best under the same conditions as most other peppers.
To avoid cross pollination, don't use the same brush or swab on different varieties. Give them each their own. A fan on the plants may blow a little pollen around, but any plant that's setting pods easily, versus a plant that's setting only one or two, is likely to have a high percentage of true seeds - if not 100% - when grow indoors.