I have attached part of an answer I gave to someone having problems focusing on a bird. This is no different than what you are trying to do with the squirrel. First off, focusing through two panes of glass is always a problem.

Factors that contribute to getting sharp pictures. A primer for backyard bird photographers.
There are two major factors that need to be considered in getting sharp photographs: accurate focus and camera or subject movement. Here are a number of things that we can do to assist us in getting accurate focus and things that we can do to minimize the effects of camera or subject movement.
Accurate Focus:
1. We need to learn to control what the camera will focus on. We do this by using “single point Auto Focus”. That is when we use only one of the many AF points available with our camera. When we take the photograph we need to be certain that this AF point is placed on the subject in the area of most critical focus. With birds, we usually use the eye or head as that location. With birds that are not moving or are only moving parallel to our position we can use “One Shot AF”. To do this we place the focus point on the critical area, half press the shutter button to lock the focus, recompose the photo if necessary, then fully press the shutter button to take the picture. We can also use AI Servo-AF if we have a subject that is moving closer to or farther away from us. With this mode, the camera will continue to adjust focus when the subject moves BUT we need to keep the AF point on the area of critical focus.
2. We need to control our aperture in order to achieve appropriate depth of field. Especially with longer focal length lenses, depth of field will be very shallow when we use the widest apertures our lens is capable of. In addition, most lenses are not as sharp when used at either extreme of our f/stop range. We therefore use the middle range of f/stops like f/8 or f/11 which will give us the best compromise between depth of field and sharpness.
Minimizing the effects of camera and subject movement:
1. Shutter speed is the single most important factor in mitigating both camera shake and subject movement. With long lenses, the rule of thumb is that you can hand hold a lens if you are using a shutter speed at least 1 over the focal length. So for a 300mm lens that means shooting at 1/300th sec. That is fine if your bird is perfectly still but birds move, feeders and tree branches can move with a breeze and if your 1/300th shutter speed is not enough to stop that motion your subject will be blurry. For birds, I suggest you double the minimum requirement. In our example of the 300mm lens, we would then need at least 1/600th sec. This rule applies even if we have Image Stabilization in our lens because IS does not help subject motion blur! In fact, I apply this rule even if my camera is on a tripod because, again, the tripod only addresses camera movement not subject movement.

2. Learn to release the shutter gently by rolling your finger across it to first get the half press to initiate focus and then to fully depress it to take the picture. Fire your camera just like you fire a rifle. Take a breath and slowly breathe out as you roll your finger over the shutter button and take the picture. This help minimize camera movement at the instant we take the picture.

3. I advocate using a tripod only for longer, heavier lenses in which case we do not lock the tripod down as we need to be able to move our camera to keep the focus point where we want it on the bird. Because of this need to move the camera the use of mirror lock up or a remote shutter release becomes impractical. When handholding the camera, brace it against something, if possible. A tree, fence post, railing, the arm of a chair, whatever is handy will help. Keep the viewfinder tight to your face, left arm bent with the hand cradling the lens from below, left foot comfortably forward, right foot back, feet at a 90 degree angle, then use your breathing technique along with the rolling motion of the shutter finger to take your shot.


Your basic settings, using a 300mm lens would look like this: 1/600th sec at f/8 at whatever ISO is needed to achieve good exposure. In bright sunlight your ISO will be around 150. If you need to adjust for lighting conditions my preference is to adjust ISO first. Only you know how high your camera will allow you to go before you get too much noise. After ISO adjust aperture and finally f/stop.

These tips are just a basic primer on getting good focus and are geared towards folks trying to take pictures of backyard birds whether they are at a feeder or perched in a tree or bush. More advanced techniques are needed for birds in flight, longer telephoto lenses and extreme distances. Since I own Canon equipment I have used Canon’s terminology. You may have to translate some of that. These are my personal thoughts based on long experience but I don’t claim any special knowledge. I welcome all additions and comments.