***** Update:
I tried your suggestion. As soon as I click (left or right) within the search pane,, the folder pane scrolls to the source bookmark, just as I'd previously described, again obliterating the view of the target folder. So, I assume you meant right clicking in the folder pane, instead. (But the act of locating the bookmark in the folder pane still scrolls the target folder out of view, regardless of how one accomplishes it!)

(And as before, when moving a lot of related bookmarks at once, a massive amount of "seesawing" is required. [for example to move 26 bookmark search results
into a target folder, one would currently:
  a) CLICK the search hit
     (causing target folder to disappear from view due to scrolling),
  b) cut,
  c) locate target folder again,
  d) paste,
    <perform 25 more repetitions of steps a,b,c,d, one repetition of each of the
    four steps for each of the remaining 25 bookmarks>

That adds up to 104 steps,
but the same results could be accomplished in three steps (selection, one cut, and one paste) with a change such as that described in item 3 below
 ] )

When I looked at the search pane's right click menu, I saw that it contains:
  Show Bookmark
  Go to parent folder
  Open
  <three other varieties of "Open">

but it does not contain "cut", unlike the right-click menu within the folder pane.
 
Although these two changes could make it unnecessary to keep locating the target folder over and over again,
  [
  1. When right clicking within the search pane, don't scroll the folder pane
   (but still do so with left clicks)
  2. Add "cut" to the search pane's right-click menu
  ],
. . .
an alternate version of that that approach would be immensely more useful:
  3. in the search pane, instead of the above two changes:
   3a. Allow use of a shift key modifier with left clicks to permit selecting
     a range of search results prior to using "cut".
   3b. When the shift key modifier is used with either left or right click,
     just select - don't "act" (don't scroll the folder pane)
   3c. Permit using a control key modifier with left clicks to select
     non-contiguous search result "hits".
   3d. Add "cut" to the search pane's right-click menu.

This change would permit moving multiple related bookmarks all at once to a single target folder using a single "cut" and a single "paste", and would solve the "back-and-forth" seesaw problem in a different manner than the one suggested in my first message.

--------------------------
****** Original message:

Nice concept. Definitely more useful than the built-in bookmark manager.

I have one major problem using it. When trying to organize a large collection of existing bookmarks, I have significant difficulty moving bookmarks into different or new folders for the common case in which each bookmark and its new folder are at a greater distance from each other than can be displayed on the screen.

One thing that might make this be easier could be the ability to drag a bookmark directly from the search results. As it stands now, when one clicks on a search hit, doing so will scroll the tree display until the bookmark corresponding to the clicked search hit is displayed.
Unfortunately, scrolling the tree display for that purpose also has the side effect of scrolling the target folder off the screen, so that it is no longer directly accessible.

One can awkwardly get around the problem by using one of two methods:
​  Method One: drag the bookmark up to the boundary between the tree display and the search-box display and wiggle it over the boundary repeatedly, causing the tree display to slowly scroll upwards until the target folder comes back into view, and dropping it onto the target once it can finally be reached.
​  Method Two: Drag the bookmark upward to a point between the top two items visible in the tree view, then scrolling the tree view until it reaches the bottom of the screen. Do this repeatedly until the target folder comes into view, and then drag one last time into the target folder.

If one could drag directly from the search frame to the target folder, such scrolling could be avoided in the case where one is moving individual bookmarks located via search..

A more general approach might be to have a menu choice when right-clicking the target folder that would cause the folder to pop up as its own window, permitting one to move one or more items from various locations within the tree to the target without having to locate both the source and target each time to facilitate each move.

In case the popup would be an implementation hassle, perhaps instead a static (unaffected by scrolling the tree) frame displaying the target folder could be the result of selecting the aforementioned right-click menu choice (instead of popping up a window, that is).

[ Note: I had originally written "implementation drag", not "implementation hassle", but changed it upon being told that it might be misinterpreted as the result of a mouse action. ]