Unlike the US (and maybe the UK?), there's no automatic bar for overstaying in Canada. Assuming you haven't worked illegally during that period, which CIC takes very seriously, and committed no crimes, you cure your overstay by simply leaving. However, the next time you enter Canada it's more dicey. You've overstayed previously, you'll be accompanying a Canadian citizen child "visiting" his father, no employment to return to in the UK...obviously, oodles of concern that you'll overstay again. This is less of a problem if you're applying for PR -- you have a kid together, there's no question that your relationship is genuine -- and plenty of visa-exempt spouses wait out their outland applications in Canada.
It sounds like you're already common law if you've been living together since summer 2012. Get your application together ASAP. It's best if you mail in your application well before your next trip back to Canada, but at the very, very least pay the filing fees online so CIC has some proof that you're serious about applying for PR. If you're nervous, fly into the US and have your boyfriend meet you in the car and drive back across one of the larger border crossings. Having your Canadian spouse/sponsor with you is helpful and crossing into Canada by land is generally considered more lenient than flying in. They can always refuse you; there is no "right" to visit Canada. However, in the latter situation (land border, accompanied by sponsor, application mailed in, visa exempt) I think refusal is unlikely. Also, keep in mind Canada is extremely lenient about PR residency obligations. You only have to live in Canada 2 out of every rolling 5 year period AND every day you live abroad with your Canadian citizen spouse counts for residency purposes...really, you can get Canadian PR and still dither about for quite some time about whether to live here or in the UK without losing it.
Flying out via the US generates "proof" of when you left Canada since the border agencies share data (as opposed to flying directly to the UK), but honestly, I think that's something they'd find out only after digging into the records. I don't think it automatically triggers something in your file that will be visible to the agent the next time you cross the border. But you did overstay. And though you shouldn't volunteer that information, if they start asking questions, you certainly can't lie about it.
BTW, I overstayed by about a year. Left to visit my parents with the kids. Hubbie filed the PR application while I was out of Canada (and therefore no longer noncompliant). We flew back to the US, he met us and drove us back across the border. In secondary the agent told me the sponsorship had already been approved and gave me a 1 year visitor record (so I didn't need to extend or leave again). You can see my timeline on the left.