Yes, Megaventory can handle that with the Manufacturing module. Below you can find two example implementations of this. The first example assumes all products in a box are the same (such as e.g. in a 'buy a six pack of beer' offer) and in the second example the bundle consists of different products (such as e.g. in a gift box)
Same contents in bundle
Let's say for example that you buy individual products with a SKU of SKU001 and you combine 24 such products and sell them in cases of 24. These cases will have a separate SKU of SKU0001-case.
You should enable the Manufacturing module in Megavetory and then create a SKU001 Simple Product and a SKU001-case Bundle Product in Magento. The SKU001-case Bundle Product will hold 24 SKU001 Simple Products.
The Magento order will go through in Megaventory as a Sales Order for the SKU001-case. Megaventory will also automatically create a Work Order to "create" this box from the 24 items (the Bill of Materials for this Work Order will be created on the fly and have a random name). When the Work Order "consumes" the components (corresponding to the Simple Products in Magento) the box will be received as a finished good (corresponding to the Bundle Product in Magento).
This feature will allow you to keep the correct stock of both the SKU001-case item and the SKU001 items (regardless of whether you sell these individually or in a bundle). This is something that Magento cannot support on its own without the Megaventory extension.
Different contents in bundle
Please go through the following video tutorials
This shows how to create a bundled product in Magento.
Magento Configurable Product to Megaventory
This shows you how to define products with multiple possible combinations without creating all of them ahead of time. Note that you will still need to create the products which are meant to be sold as a bundle. Those products which are actually created will actually sync to Megaventory too.
This demonstrates how a visitor of yours can purchase a bundle and this will create a Sales Order both in Magento and Megaventory and also a Work Order in Megaventory. Processing the Work Order in Megaventory (ie packaging the goods) will reduce the stock of the raw materials and increase the stock of the finished good (the bundle).
Processing the Sales Order in Megaventory will reduce the stock of the finished good (ie the order will be fulfilled). The Order status will be synced to Magento as Shipped too. Overall, that way you'll be able to sell and track the stock of both the components and the bundled products.
Obviously, the above are indicative of the process - you may want to apply other attributes or dynamic pricing etc in your specific Magento setup. This article should clarify the fundamentals however.