How do I avoid having to do this >> http://prntscr.com/bl1k5h when making a map? Notice the overlapping bonuses. Do I have to outline the entire continent and then break away sections of it to avoid this?

Do I have to outline the entire continent and then break away sections of it to avoid this?

yes

Use this https://docs.google.com/presentation/d/1NTfstv7aP0zAOMnjkY0AR8BNM-v3pYbxbjvckyxgwII/edit#slide=id.g132d0e1f17_0_52
or follow this:
1) make big territory representing a super bonus
2:
a) draw a line across where a bonus border will be (making it a bit longer at both ends)
b) do path > stroke to path
c) Shift-click super bonus
d) do path > difference
e) do path > break apart
f:
i) draw a line across where a territory border will be (longer at both ends)
ii) shift-click bonus
iii) do path > division
iv) repeat for all territories in bonus
g) repeat for all bonuses in super bonus
3) repeat for all superbonuses