Force iphoto to store all photos in library

I have iPhoto 9 running on a brand new MacBook Air, and my problem is twofold.
Firstly, when I initially created the library, I imported the photos from a variety of folders copied onto an external HDD (which is the location of the iPhoto library too, for information purposese).  However, the 'copy files to iPhoto library' option was not checked, so it appears on first impression that the files are referenced and not stored.  I realise this was a mistake, not least because all the sorting and deleting I have done within iPhoto is a waste of time, because I have to keep the original folders and cannot delete them, because iPhoto cannot find the files if I do.  So the first question is 1) can I force iPhoto to copy all the photos from the original location to its own library so they are not referenced, but managed files?  I have tried checking the option to 'copy imported photos into iPhoto', shutting down then restarting in the hope it would do this, but when I delete the original reference folder from which they were imported, iPhoto wont find them - so clearly it hasnt worked.  I cannot believe that I will have to start again and there isnt a way to now force iPhoto to just store all the photos it uses, within its own library and allow me to delete the original folders. Can anybody help?
Secondly, I am trying to create a Photobook from within a piece of Third Party software - When I navigate to the 'Masters' folder in iPhoto it wont allow the files to be previewed and dropped into the photobook.  So if I do all my photo management within iPhoto, is there any way to be able to view the photos in a finder style window from within the third party software (which for information is CEWE Photoworld, built for Mac)?  It seems rather ridiculous that if you manage your photos in iPhoto, you cannot then view them in anything else, or do anything with them.  There must surely be some way to open the library and be able to 'use' my organised and edited photos elsewhere...? Otherwise the software I am trying to use is completely and utterly pointless, as most people will presumably use iPhoto (being free and part of the basic Mac software package) as their photo management and editing suite.  To say I am frustrated is an understatement.
Hoping somebody can come to the rescue and sort these problems out.
Thanks in advance.

You can get all of the photos into the library by setting iPhoto's preferences to copy during import.  Then do the following:
Using iPhoto Library Manager  to Rebuild Your iPhoto Library
1 - download iPhoto Library Manager and launch.>Click on the Add Library button,
2 -  select the library you want to add from those in the selection window.
3 - make sure that in the rebuild window the checkbox  "Scavange orphaned photos" is checked.
4 - now that the library is listed in the left hand pane of iPLM, click on your library and go to the Library ➙ Rebuild Library menu option
5 - in the next  window name the new library and select the location you want it to be placed. Click on the Create button.
Note 1: This creates a new library based on the LIbraryData.xml file in the library and will recover Events, Albums, keywords, titles and comments. However, books, calendars, cards and slideshows will be lost.
Note 2:  Your current library will be left untouched for further attempts at a fix if so desired.
The rebuild library will have all of the photos imported into the library.  If you can live with the loss of the projects, i.e. books, etc., keep the rebuild library and delete the old library..
As for accessing the photos for the 3rd party application you do not need to access the Masters folder via the Finder and should not.  You can drag a photos from the open iPhoto window into the other apps window or use one of the methods described in the following User Tip by Terence Devlin :  How to Access Files in iPhoto

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