Ok so i have the character laying on her back looking up. I have animated her having a nightmare and then waking up wide eyed. I then want her to sit up in bed. I have found the mixmove_female titled "lie01_to_sit04_ which i have placed after laying/nightmare animation, and when i play them she rotates on the spot between the clips, when all i want is them to blend together seamlessly. So it seems like she is naturally aligned differently? I have tried lots of different things such as playing with the motion settings options under the animation tab. I've tried just rotating her to align with the direction of the original clip but that doesnt work. Can someone please help me figure this out? I would be eternally grateful! Oh also i have googled for an answer but no luck really.

Mix Moves work best when used together. To save the hassle you should have been using Lie01 for her lie down and then animate nightmares.
But you can still use them with your own clip. 
What you have to do, is to use collect clip and save your initial clip as Motion Plus. That would reset a lot of things internally.
Then delete original animation, uncheck "Align to Actor Orientation", "Reset Motion Root" and "Reset Motion Root Rotation".
After that make sure the character is at the default T-pose at 0,0,0  and apply saved Motion Plus clip. At this point your original animation should be reinstated as before.
Finally apply Mix Move clip at the end  and use Align > Root from right mouse click context menu.
If you have some odd Z rotation (which even present mixing Lie01 with Lie01_to_sit04), then rotate Hips in Edit Motion Layer (FK mode) by Z at the very first frame of the second clip (to align with first clip).

Legend! 

Thank you for your detailed response! I'll give it a go :)