First you are going to have to write out the question clearly. You say first

" We introduce x1=x(t) x2=x'(t) x3=x''(t) "

which has x as dependent variable and t as independent variable, and then

"because my 2 equations contain dy/dx and d2y/dx2 terms I assume I have to introduce y1=y(t) y2=y'(t) y3=y''(t)" where your equation seems to have y as dependent variable and x as independent variable but then you have switched to "t" as independent variable in the second line.

What is the specific problem you are trying to solve?