How do I resolve the unrecognized plugins by BOSS?

Use LOOT instead of BOSS. BOSS and its masterlist of mods (which specifies how mods are to be optimally sorted) are no longer being maintained for Skyrim. LOOT does the same thing as BOSS, which is to optimally sort the load order of mods/plugins, and it is still being maintained for Skyrim.

According to BOSS' webpage (emphasis mine):

Using mods for Skyrim, Fallout 3 or Fallout: New Vegas? Use LOOT instead, as BOSS's support for those games is relatively poor and no longer maintained.

The BOSS message about "positioning manually" is because the mods' load order have to be sorted manually by the user as they are not in the (unmaintained) BOSS masterlist. "Submitting the URL of the mod" is supposed to be for the maintainers of the masterlist, so they can check the mod itself and verify its optimal load order and update the masterlist to include the mod's data. Since the BOSS masterlist is no longer being maintained, submitting the URL is pointless. You don't need to do either of these if you switch to using LOOT instead.

See LOOT's FAQ page for more info:

Moving From BOSS

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Do I have to switch from BOSS to LOOT?
No. However, BOSS is no longer maintained for games other than Oblivion, and LOOT generally provides superior functionality.

Is there anything I should bear in mind when switching to LOOT?
It's worth double-checking the load order LOOT gives you, in case it's gotten something wrong. Also, if you're not starting a new game, changing your load order may cause in-game issues. To avoid disaster, you can backup your load order as follows:

1. Make a backup of your current .ess save file, and its accompanying .skse file (if you have SKSE installed). These are found in the %USERPROFILE%DocumentsMy GamesSkyrimSaves folder.
2. Make a backup of your load order files, plugins.txt and loadorder.txt , which are found in the %LOCALAPPDATA%Skyrim folder.

That way, if something does go wrong, you have backups to roll back to. If you don't overwrite or delete save files, you don't need to back them up, so long as you can remember which save was made before you made the changes that caused problems.
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How can LOOT not have unrecognised plugins?
To sort a plugin, BOSS needs it to be added to its masterlist, which is hand-ordered by its maintainers. LOOT instead reads the contents of each plugin to see which plugins conflict, etc. and uses that information to decide on the best ordering. This means that it can sort all plugins without needing them to become recognised first.

Does LOOT sort based only on plugin content?
No. While it can sort most plugins correctly, sometimes it gets things wrong, and LOOT's masterlist is used to provide metadata so that it can sort such plugins correctly. Unlike in BOSS, LOOT's masterlist doesn't give specific load order positions, which makes it more adaptable and easier to maintain.

How can the load order LOOT gives be right if BOSS gives a very different load order?
There can be more than one correct load order for a given set of plugins. For example, some plugins may not conflict or depend on each other, so their relative orders wouldn't matter. The load order BOSS gives is hand-made to look 'neat' as well as work, so plugins from the same mod will usually get grouped together, but LOOT doesn't know which plugins belong to which mod, so it just puts them where it thinks they work.