Unfortunately, you cannot use the Eclipse SmartHome Designer (ESHD) to edit openHAB 2 Things and/or Items (and their links to channels) if you have used PaperUI to create them, since this info are saved in the JsonDB Storage (which is not an RDBMS… that would be too heavy)
ESHD works with the configuration files in your OPENHAB_CONF folder (e.g. /etc/openhab2/ in Linux apt based installation).
There is no editor (currently) for JsonDB files which store configuration data for Things, Items and Links.
You can manually edit them but it’s not easy… you are right. By the way, the doc entry for JsonDB has been updated and will be further enhanced soon: http://docs.openhab.org/administration/jsondb.html
Regarding ESHD: I recommend to use release 0.80. There are some issues (can’t find the link atm) with the snapshot 0.90 release. (I know… the docs recommend the nightly snapshots build)
I am planning to post an update to that thread (how to manage the confs) which will include some additional info on JsonDB and other stuff. I tackled only a small part at that time (configurations for bindings).
Since you are an advanced user of computing systems: you could switch to manually defined Things & Items and then use ESHD to work with them.
I do this (with the exception of Z-Wave Things) and I mainly use ESHD to verify syntax for all my OH2 stuff (things, items, sitemaps & rules)