I found areas of interest on Google Earth, I saved the waypoints under .kml I then converted .kml to .gpx which allows me to upload into my Humminbird Helix 12. The problem I'm having it's not uploading everything.

Any advice please.

A Helix will not load GPX files. The data has to be in a MATRIX folder for the unit to recognize it.

Install HumminbirdPC on your PC, load the GPX file to that, then use the memory card symbol on the left of the panel to copy the file to a memory card that is 32GB or less.

+1
WARNING
HBPC will hang or report a corrupted GPX file trying to open when the Google Earth created waypoints don't have a date in the date-column.
Initially HBPC will open the "foreign GPX" file and you can upload the MATRIX folder to your SD-card, but after you close HBPC and later restart HBPC it will report a corrupted file or hang. Solution is to download the SD-card back into HBPC creating a new "HBPC GPX" file and delete or close the "foreign GPX".
WARNING

GE Tips:
Have waypoint names on the Google Earth items, which will allow you to sort them into "like categories" in HBPC which will allow you to bulk-edit icons.

Zoom-in as much as possible to place the GE waypoint for better accuracy. Also center the GE placement cross-hairs on the target. Don't use the tip of the "default pin icon". I find resetting GE to use the circle icon best.