Hi,
Create a part in an assembly with default constrained which would be you pipe. Then activate the part and create a pipe feature and use only points one on each fittings and be sure to choose spline before adding the points. Now you can see that the pipe is tangential to the fittings. Now "Redefine" the feature and can select the starting and ending of the pipe to be normal to a surface.
Make sure that the pipe function is not used in assemble mode instead the pipe feature has to be created in a part in the assembly. The part gets activated and then you can create feature.
Hope this helps