I came up with this little script

url='https://www.mywebsite.com';
await page.goto(url, { waitUntil: 'networkidle0' });

await page.type('#logonIdentifier', '[email protected]');
await page.type('#password', 'mypassword');
await page.screenshot({ path: '/puppeteer/step01.png'});
//this is where i handle popup windows
page.on('dialog', async dialog => {
    console.log(dialog.message());
    await dialog.dismiss();  // or await dialog.accept()
	});

await page.click('#next'); 
await page.waitForNavigation(); 

console.log(await page.content());
await page.screenshot({ path: '/puppeteer/step03.png'});