Everytime I exit the program and reopen my work it moves the equations and solutions arround so I have arrays over two diffrent sheets.
This sounds like a bug in th software - it should keep your formatting of course. I read here already about formattting problems with inserted graphics but now the first time about probs with math regions.
How can I save it and keep my format in place other than saving as a pdf
If its a software bug ther is not much you can do, I guess. Report to PTC stuff and hope its addressed in a future version.
Would using Mathcad15 instead of Prime2 be an option? MC15 is superior to P2 anyway.
Also a section of it has some fairly lengthty equations, and I was wondering if there is a way to decrease the math font size or change the orientation for only certian sheets?
Not yet, math formatting is to be expecting in version Prime 3 which should be released this summer. Don't think that changing the orientation for selected pages would be possible, though.