Spend some time to integrate those things together, in other words to generate pdf in javascript and save it to filesystem.

Actually there is nothing hard, but I will describe how you can make it work. Hope this will save somebody's time.

At first you need to add to cordova FileSystem plugin. It's can be easily done with command line:

cordova plugin add org.apache.cordova.file

Also you need to patch jsPDF (I'm talking about version 0.9.0), because it doesn't work on android with default blob creation.
You need to replace commented line with following code (thanks to stackoverflow answer http://stackoverflow.com/questions/18596005/generate-client-side-pdf-with-jspdf-on-phonegap-based-apps):

//                    blob = new Blob([array], {type: "application/pdf"});

try
{
    blob = new Blob([array], {type: "application/pdf"});
    console.debug("case 1");
 }
 catch (e)
 {
     window.BlobBuilder = window.BlobBuilder ||
                                          window.WebKitBlobBuilder ||
                                          window.MozBlobBuilder ||
                                          window.MSBlobBuilder;
     if (e.name == 'TypeError' && window.BlobBuilder)
     {
         var bb = new BlobBuilder();
         bb.append(data);
         blob = bb.getBlob("application/pdf");
         console.debug("case 2");
      }
      else if (e.name == "InvalidStateError")
      {
          // InvalidStateError (tested on FF13 WinXP)
          blob = new Blob([array], {type: "application/pdf"});
          console.debug("case 3");
       }
       else
       {
           // We're screwed, blob constructor unsupported entirely
           console.debug("Errore");
       }
 }

And the last step will be actually generate and save created file!

// Somewhere in your code
window.requestFileSystem(LocalFileSystem.PERSISTENT, 0, gotFS, fail);

function gotFS(fileSystem) {
    fileSystem.root.getFile("test.pdf", {create: true, exclusive: false}, gotFileEntry, fail);
}

function gotFileEntry(fileEntry) {
    fileEntry.createWriter(gotFileWriter, fail);
}

function gotFileWriter(writer) {
    var doc = new jsPDF();
    doc.setFontSize(14);

    doc.text(20, 20, 'Hello world!');
    writer.write(doc.output());
}

UPDATE 21.03.2014
Last version was producing corrupted PDF, below is updated code which works properly with images using jsPDF.

var sourcer = $('#imageForDocument');

function writeReport(doc) {
    var data = doc.output();
    var buffer = new ArrayBuffer(data.length);
    var array = new Uint8Array(buffer);
    for (var i = 0; i < data.length; i++) {
        array[i] = data.charCodeAt(i);
    }
    writer.write(buffer);
}

if ($("#doclogo").length > 0) {

    window.canvasplugin(sourcer.attr('src'), function (val) {
        var doc = makePdfReport(val);
        writeReport(doc);
    });
}