No, only the ordinary income portion is taxed at the 12% rate. Long term gains are taxed at 0% up to that $39,375 point. That's the "layered" reference I mentioned. E.g. you could have $39,375 of ordinary income, reduced to $27,375 with the $12k standard deduction, taxed at a 12% rate (marginal, not total tax rate) allowing $12k of capital gains to be realized and taxed at 0%. Warning, that is a VERY oversimplification of how it works and you might have other factors but that basically how it works. And it only applies to federal taxes.
Edit: The challenge is to get a good estimate of what those ordinary income items will be. If you miss something and it puts you over the limit, only the amount of capital gains over the limit will be hit with the 15% tax rate. Again layered: e.g. $45,000 ordinary income less standard deduction ($12,000) = $33,000. If you underestimated and still realized $12,000 of long term capital gains, you would pay 0% on the $6,375 of the gain and 15% of the rest (math might be off but you get the idea I hope.)