I am applying for the pediatric subspecialty match. I am having trouble understanding whether I should apply to both the MOH funded and non-MOH funded spots or only the MOH funded spots in Ontario....

If you are eligible for the Ministry of Health and Long-Term Care (MOH) funded positions, then you can apply to both streams. Below is how the province of Ontario for example, breaks it down.

MOHLTC – Funded positions
PGY3 residents with completion dates between July 1 and December 31, are eligible but must declare their completion date on the application form and request a late start. You may only apply to the match one time.
Pediatric residents with completion of PGY3 training after December 31, should apply to the next upcoming match.

Non MOHLTC – Funded positions
Current residents who will be completing PGY3 training or PGY4 training in Core Pediatrics on or before June 30 are eligible.
PGY3 and PGY4 residents with completion dates between July 1 and December 31 are also eligible but must declare their completion date on the application form and request a late start. You may only apply to the match one time.
Pediatric residents with completion of PGY3 training after December 31, should apply to the next upcoming match.

Quebec, also has two streams:
Contingent régulier is for residents completing their programs in Quebec and the contingent particulier for medical residents completing their programs outside of the province de Quebec.