My question has two parts one is sort of a hijack so sorry but hopefully someone can help me out.

I departed Yellowknife a week or so ago and was filed on a composite flight plan from Yellowknife to Cambridge Bay the YZF portion was IFR. The flight planned altitude was 9000ft .

My departure clearance was flight planned altitude to YCB via Yellowknife sid one.
which is runway heading to 4000ft or flight planned alt which ever is lower. On departure contacted Edmonton center and was told '' Runway heading to 5000 not above 9000 in controlled airspace"

My question is the controller expecting me to maintain 5000 or is he expecting me to climb to 5000 then turn on course and maintain 9000. I was about to ask when the controller cleared me present position direct and maintain 9000 so the altitude never came into play.It seems to me maybe something was missing in the clearnce airbourne. Is it because he wanted runway heading to 5000 and just put the 9000 in case of a comm failure. Really not sure but any comments would be great.

My other question is if the aircraft is not GPS certified is it riskey accepting "present position direct"

Sounds like sloppy phraseology to me. I would guess you were cleared to 90 and runway heading out of 50 but in a case like that I would ask for clarification.

Should have been something like

"ABC maintain 90 while in controlled airspace, leaving 50 proceed direct XYZ"

As for accepting direct somewhere down the road without being able to...........DON'T!!
Tell the controller you are only standard equipped and need airways or a heading. Here's the difference for us in a non radar environment. GPS aircraft direct somewhere we protect 10 miles either side of track, standard equipped aircraft on a heading to a VOR we protect 45 miles either side of track.

That's what I was thinking and I was just going to ask before 5000, just wanted to make sure I wasn't missing something. Thanks for the response and the GPS direct info is good to know. The airplane has two certified IFR GPS but the crew are not certified so I guess I just answered my own question.

Sounds like he wanted you to go runway heading to 5 then proceed on course. The RH to 5 would be to allow for another a/c on a crossing runway to get a 'clearance valid' so we could launch him off the crossing runway on the Yellowknife One to 4000.