As @Darren_Poulson said, the UIs are quite helpful for a lot of things but they are not there yet to cover all aspects of the configuration. You want to build rules and sitemaps in configuration files. See the documentation here for all details regarding configuration: http://docs.openhab.org/configuration/ (your question 3)
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Persistence is great for a lot of things but I’d recommend to look into it later. You first need to have a working home automation before you can persist data over time and do something meaningful with it. When the time comes, you should look into the InfluxDB+Grafana Tutorial
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Yes. There is a Tutorials section here in the forum with many great examples to look into and learn from. A list of selected examples can be found here: http://docs.openhab.org/tutorials/
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@chris is the right one to respond to your observation…