I *know* this should be simple: aligning logo

IMO the best way to do it is with a script.  A script can resize you logo to an appropriate size for the image receiving the logo. And Aligned to where you want it aligned. The script I have posted is easy to modify for your logo and the size you want but I chose to align the logo to the bottom right.   I have also posted had yo do ir with and action.  The action dos align the custom logo to the bottom left.

Crafting Actions Package UPDATED Aug 10, 2014 Added Conditional Action steps to Action Palette Tips.
Contains

• Action Actions Palette Tips.txt
• Action Creation Guidelines.txt
• Action Dealing with Image Size.txt
• Action Enhanced via Scripted Photoshop Functions.txt
• CraftedActions.atn Sample Action set includes an example Watermarking action
• Sample Actions.txt Photoshop CraftedActions set saved as a text file.
• More then a dozen Scripts for use in actions

Example

Download

My Script PlaceWatermark.jsx

#target photoshop;  
app.bringToFront();  
var logoFile = "~/Desktop/JJMack.png"; // Watermark file should be large for resize down works better than up
var LogoSize = 10; // percent of document height to resize Watermark to
var LogoMargin = 1;                                         // percent of Document height the Watermark should have as a margin
placeWatermark(logoFile, LogoSize, LogoMargin);             // Place Watermark  into the bottom right of document
function placeWatermark(Image,Size,Margin){  
  if(!documents.length) return;   // if no document return
  try{  
  var doc = app.activeDocument; // set Doc object to active document
  app.displayDialogs = DialogModes.NO; // Dialog off 
  var strtRulerUnits = app.preferences.rulerUnits; // Save Users ruler units 
  var strtTypeUnits = app.preferences.typeUnits; // Save Users Type units 
  app.preferences.rulerUnits = Units.PIXELS; // work with pixels 
  app.preferences.typeUnits = TypeUnits.PIXELS; // work with pixels 
  var fileObj = new File(Image);                 // the passed file
  if(!fileObj.exists){   // If file does not exits tell user 
  alert(fileObj.name  + " does not exist!");  
  return;  
  }  
  placeFile(fileObj); // Place in file the Watermark png file
  activeDocument.activeLayer.resize(100 ,100,AnchorPosition.MIDDLECENTER); // Insure Place did not scale layer  
  var SB = activeDocument.activeLayer.bounds; // get layers bounds 
  var layerHeight = SB[3] - SB[1]; // get layers height  
  var resizePercent = (100/layerHeight)*(Size/100*doc.height.value); // Percent to resize by 
  activeDocument.activeLayer.resize(resizePercent ,resizePercent,AnchorPosition.MIDDLECENTER);  // Resize width and height by percentage 
  SB = activeDocument.activeLayer.bounds; // get resized layers bounds  
  activeDocument.activeLayer.translate(-SB[0].value,-SB[1].value); // Move resized layer to top left canvas corner 
  var LayerWidth = (SB[2].value - SB[0].value);  
  var LayerHeight = (SB[3].value - SB[1].value);  
  marginSize = Margin/100*doc.height.value; // move resized watermark into the document lower right corner with some margin
  activeDocument.activeLayer.translate((doc.width.value -marginSize - LayerWidth),( doc.height.value -marginSize - LayerHeight));
  }
  catch(e) { alert(e + ': on line ' + e.line); } // inform user of error  
  finally{  
  app.preferences.rulerUnits = strtRulerUnits; // Restore user ruler units  
  app.preferences.typeUnits = strtTypeUnits; // Restore user type units    
  };  
}; 
function placeFile(placeFile) {  
    var desc21 = new ActionDescriptor();  
    desc21.putPath( charIDToTypeID('null'), new File(placeFile) );  
    desc21.putEnumerated( charIDToTypeID('FTcs'), charIDToTypeID('QCSt'), charIDToTypeID('Qcsa') );  
    var desc22 = new ActionDescriptor();  
    desc22.putUnitDouble( charIDToTypeID('Hrzn'), charIDToTypeID('#Pxl'), 0.000000 );  
    desc22.putUnitDouble( charIDToTypeID('Vrtc'), charIDToTypeID('#Pxl'), 0.000000 );  
    desc21.putObject( charIDToTypeID('Ofst'), charIDToTypeID('Ofst'), desc22 );  
    executeAction( charIDToTypeID('Plc '), desc21, DialogModes.NO );  
};  

Open the file that is transparent and has a logo in the lower corner. Also open the file you want to add the logo to.

Window > Arrange > 2-up Vertical.

Select the Move tool. Hold the Move tool down on the logo (not the transparent area).

Keep the mouse down and drag the logo over the other file. Once the cursor is over the other file, hold down the Shift key and then release the mouse. The Shift key will maintain the same position.

.

Use paste in place.