Hi
For the issue with inventory you need to ensure you add the single box SKU as the component of the multi packs with the relevant quantity.
Shopify native bundles let you link all components of a variant and this then shows up during checkout and as separate order lines in admin. This means all inventory is kept up to date by Shopify directly so you don’t need to rely on an inventory app.
The free Shopify bundle app won’t let you make these kind of variant set ups but you can use our Bundle Sync app which lets you set these up using the Shopify structure. You can set up each variant in Bundle Sync through the interface or you can manage all bundles using a csv file to make bulk updating easier.
In terms of subscriptions I don’t think you can add one as part of a bundle as they are different kinds of products and Shopify only lets you add product variants as components.
Regards
Sam