I am a new PR Canadian resident with a US passport. As you can imagine i go back and forth from time to time between both countries, sometimes I fly in to Canada and some times I drive out. or viceversa. I rarely get stamped or checked at either border.
How Do i prove that I never left canada or that I ever came back? or asked differently, how does Canada ever know I left?
You inform them. It is up to the PR to provide this information.
Burden of proof is always on the PR. Either when you apply for a new PR card or for citizenship. Or, if for some reason there is a question about Residency Obligation compliance when returning to Canada upon arriving at the PoE.
Best to keep a complete and accurate log of all border crossings in order to do this. Even a cross-border commuter should keep a precise log (think of the kind of log a trucker is required to keep), probably especially so, despite how voluminous it is.
Whether or not, and when, Canada might identify errors in your accounting is difficult to forecast. Obviously, even though minor discrepancies are typically considered to be incidental error, the discovery of substantial discrepancies could be approached as misrepresentation. Best to not go there, not anywhere near there.
In particular, any omissions can cause IRCC to question the PR's credibility. If IRCC apprehends a deliberate omission, consequences can range from compromised credibility, to inadmissibility proceedings and loss of PR status, to (in the more egregious cases) prosecution of criminal offence.
How Canada might discover discrepancies with actual facts is a huge subject, too many variables and nuances to get distracted chasing down that
rabbit-hole. There are enough ways to make it worth the PR's while to not test it, to avoid conflicts between the PR's account and the actual facts by keeping a complete and accurate record.
Gathering and Maintaining Proof:
Other than, that is in addition to the travel log, most PRs do not need to keep any more than the usual records a person keeps, pertaining to employment, taxes, and home. These things create enough of a paper or printable-digital trail for anyone living and working in Canada.
Always present the PR card upon returning to Canada. These days the entry is almost always captured and becomes part of the PR's CBSA travel history. So IRCC and CBSA will usually be able to see the dates (and PoE) of every entry, or at least almost all of them. For frequent cross-border travelers this actually creates a more complete picture of time in Canada even if entry dates into the U.S. are not readily accessed (last I knew, the respective governments were still working out the details of information sharing relative to citizens . . . Canada now has relatively-easy access to the entry-into-the-U.S. history for non-citizens of the U.S.), recognizing that sometimes IRCC will request the PR to personally obtain and submit the U.S. history.
PRs who are not well-settled and working in Canada, would be prudent to take extra care to document their presence. The more frequent or longer the PR spends abroad (including in the U.S.), the more extensively so.