Setting up your products to be in bundles involves creating a "Bundle group" in the app where products from the store are selected and a discount is set to apply when an instance of each of the selected products are added to the cart. When the group is created the app will then create app variants to represent the cheaper variant pricing that a customer would get in the cart when eligible for a bundle discount. To set this up, perform the following:
1. Open up the app admin.
In your stores Shopify admin, go to the "Apps" section, find the Product Bundles app, and click on the app's title to open up the app admin.
2. Begin to Create a New Bundle Group.
In the app admin, click on the "Product Bundles" link in the main navigation in the app admin.
You'll be taken to a new page, which will list all currently created bundles groups, and allow you to create new ones. To create a new group group, click on the green "Create New" button.
3. New Bundle Group: Step 1 - General Options.
In this step you set some of the basic settings that will apply to this bundle group.
In the internal name field, give the group a name that will help you identify what this group is about. A good naming convention is to name the group off of the products that you'll be selecting in it. For example if you want to put a pair of shorts and a t-shirt in a bundle, you could call it shorts/t-shirt bundle.
Input a "bundle widget title". This is literally the text that will appear at the top of the bundle widget as a title on the product pages of the products that this group has selected.
For the "Apply Product Bundle" section, select whether you want to bundle across products or bundle across collections.
Selecting "bundling across products" will allow you to put two or more specific products in a bundle and the customer can only get a bundle discount with those selected products.
Selecting "bundling across collections" will allow the customer to be able to pick their choice of a product from each collection you select to be in the bundle.
Select one or the other according to your needs and proceed to the next step.
Please note that a current limitation of the app is that you can't bundle two of the same products together, or have the same product in two or more active bundle groups. Consequently you wouldn't be able to bundle the same collection together, or two collections that contain the same product.
4. New Bundle Group: Step 2 - Select products or collections to include in the bundle.
Please select the tab according to what you selected in the "Apply Product Bundle" section from the above step.
In this step, select the products that you want to participate in a bundle group. To start the process, click on the "Select Products" button. 
Clicking on the "Select Products" button will open up a product selector where you can select specific products. By default the stores entire store list will appear in the list of products, but you're able to filter the list by collection, vendor, type, etc., as illustrated in the image below. Once you select a product click on the green "Continue with selected products" button.
The product selector will close at this point. You'll be able to change the displayed product title and image in the bundle widget as pointed out below:
You'll need at least two products in the bundle, so repeat this process one more time.
When you're done adding products to the bundle, input a percentage discount that you'd like to apply to each product of a completed bundle in the input field that is labelled "Enter Bundle Percent off".
In this step, select the products that you want to participate in a bundle group. To start the process, click on the "Select By Collections" button.
Clicking on the "Select by Collections" button will open up the collection selector to assign a collection to the bundle. Click on the title of a collection to select it. Click on the green "Select Collection" button to continue with the selected collection.
Doing so will close the collection selector. At this point you'll be able to change the collection title and image of the collection in the bundle widget. Click on the green "+" button to save the collection and it's details.
You need to have at least two collections in the bundle so you'll need to repeat the process one more time.
When you're done adding collections to the bundle, input a percentage discount that you'd like to apply to each product of the completed bundle in the input field that is labelled "Enter Bundle Percent off".
5. New Bundle Group: Step 3 - Configure Display.
In this step you simply select the style of the bundle widget that'll show up on the product pages of the product's that you selected in "Step 3 - Select Products".
6. New Bundle Group: Create and test!
When you're satisfied with the information you entered then you may click on the green "Create" button at the bottom right hand side of the page to save the group. If a pop up box appears stating that there was some problems validating the data, then it's most likely because one or more of the sections weren't filled out entirely, and in the that case, please review each section to ensure that you entered all required information, and try again.
If there's no validation errors you'll be taken back to the "Product Bundle Groups" page where your new group will be listed, which you can then edit further at any time. The app will take at least the next few minutes going through the selected products, creating app variants and the bundle widgets for each of them, which at that point they'll be available on the store front. It's a good idea at that point to go to the storefront and test the Product Bundles functionality to ensure that everything is working properly.