Went with doing an iframe rather than a new window:
function runUpdateWindow() {
var frame = document.createElement('iframe');
frame.src = "www.mydomain.com/secondpage";
document.body.appendChild(frame);
var frameWindow = frame.contentWindow
var updateSQL = 'UPDATE TABLE...';
frameWindow.onload = function (){
var textarea = frameWindow.document.getElementById("BUpdates_SQL_Statement");
var button = frameWindow.document.getElementById("BUpdates_Submit");
textarea.value = updateSQL;
frameWindow.v$('BUpdates_Submit').click();
};
}
a huge thank you to Dagg Nabbit for helping me figure this out!