Ask Microsoft if the company has plans to get into the vertical-application space — by selling healthcare software or pharmaceutical applications, for example — and the company's pat answer is only via its software and reseller partners. But the real answer is much more complicated.

Microsoft Business Solutions, Microsoft's small/mid-size business division, is adding more layers to its software stack upon which it is encouraging independent software vendor (ISV), system-integration and reseller partners to build.

Traditionally, Microsoft has encouraged partners to build their solutions on top of Windows. Last year, Microsoft one-upped this proposition, by publicly encouraging its partners to build their vertical applications on top of not just Windows, but also other Microsoft technologies, such as its MS CRM and Microsoft Business Framework layers.

Now, Microsoft is adding yet more of its own technologies to the stack atop which it is suggesting its partners build. It is suggesting that ISVs and other channel partners use Microsoft Business Solutions' bill-of-materials, project-accounting, payment-processing, core transaction-processing and EDI distribution modules from its Great Plains, Navision and Axapta products as the foundation for their own products. Microsoft officials are advocating that partners either embed these Microsoft modules right into their own vertical products or customize their applications in a way so that they only work atop these Microsoft modules.

Microsoft is calling this new layer of technology its "industry-enabling layer."

"In some cases, (the parts) of this industry-enabling layer exist already. In others, we will build or buy the technologies," said Glenn Bray, director of vertical strategies for Microsoft Business Solutions.

Last week, Microsoft invited about 150 of its ISV partners to its Redmond headquarters for two days to hear first-hand its industry-enabling-layer proposal, as well as about its future marketing and evangelism plans. Company officials outlined new Microsoft beta programs, such as its Technology Adoption Program (TAP), as well as the less-exclusive "Ascend" and "Touchdown" beta programs that are for ISVs only.

At the so-called "Apex" ISV meeting, Microsoft officials also outlined its plans to take its ISV message on the road via a 11-city road show that will commence in Sydney, Australia, later this month.

Read More Specifics on the ISV Road Show Plans Here

Microsoft isn't the only major software vendor wrestling with how to avoid competing with its software partners, while growing its vertical-software business.

Late last year, IBM acknowledged it has plans to push deeper into a dozen or so key vertical markets. In February, IBM rolled out middleware tailored to the first of these verticals — financial services firms, banks and insurance companies.

Read More on IBM's Push Into Verticals Here