[UPDATE] If you have updated to iOS11 then the original iThoughts (blue and orange icon) will not run. In that case, please take a look here for instructions.
There are a number of ways to migrate your maps from the original app into the new app.
if you already have a 'cloud folder' synced to Dropbox then you can create a similar setup in the new version and have it sync your maps down - see this article on cloud synchronisation.
iOS7, 8, 9, 10
If you are not syncing (with Dropbox) then you can use the 'Send Archive -> ...to App' feature in the original version to send an archive (COPY) of all your maps over into the new app. See below.
If the above doesn't work...
You can use the 'Send Folder to Cloud' option to upload all your maps to Dropbox (in ITMZ format) then in the new app download all those maps - or better still, set it up to sync - see this article on cloud synchronisation.
Open each map and use the 'Send Email' option to email the ITMZ of the map to yourself - then tap on the attachment (in Mail on your iPad) and elect to open it in the new iThoughts.
NB: To see the archives in the original app you'll need to append /backups on the website address - for example http://192.168.0.6:44444/backups
If all else fails, drop me a line (there are other 'avenues')