But Pritchard says there aren't many firms like his that target mid-market or small companies and focus on corporate debt or convertible securities transactions. Pritchard spent ten years at Jefferies as a specialist in this sector and his co-founder, Cunningham, spent 18 years at Jefferies, rising to head its convertible securities division. They've been running Aequitas (Latin for “fair trade”) for a year and a half.

“Our motto is that an informed issuer will obtain the best results,” says Pritchard, who sees an inherent conflict in the investment banking industry's debt issuance process.

There's a common misconception among corporate executives that once a company selects an investment bank, the bank is working solely on the company's behalf as it issues the company's debt, he says. “What companies need to appreciate, perhaps more fully than they do, is that when they retain an investment bank to do a financing for them, that bank is going to sell that company's securities through their own internal sales force, who have an allegiance and loyalties on the opposite side of the transaction, while the investment banking group has allegiance to the corporate issuer.”

Pritchard is quick to say that this does not mean that banks are up to no good, but he notes that many investment banks “may do some of their best work when they know they are being closely watched.”

So how can advisory firms such as Aequitas help corporations?

Michael Biehl, CFO at Chart Industries, a Cleveland, Ohio-based manufacturer of equipment for the industrial gas industry with $794.6 million in 2011 revenue, and an Aequitas client, says having an adviser “looking over your shoulder” can make the bank selection process far more competitive and weed out banks that are not up to snuff or familiar with more complex deals. Once the selection is made, an independent adviser can monitor the bank and its marketing efforts, says Biehl, helping to make sure the bank is doing the most for the company's issue at all stages of the process.

Biehl, pictured at right, says he also benefitted from having Aequitas talk to his company's board about the complexities of a recent refinancing, explaining all of the risks in detail. “You need someone who can provide support to your team but can also give the board comfort in terms of the complex deal process, how it works and what to expect.”

Pritchard says Aequitas does its best work when it is brought in early in the process. “We want to help companies manage the competitive dynamics during the bank selection process—known as a 'bake-off'—when investment banks come to offer their services, helping the issuer to win a more favorable fee,” he says, noting that there are both direct and indirect costs associated with debt deals.

CFOs or their advisers should be negotiating not just for lower fees and better deal structures during the bank selection process, but also lower interest rates on the debt, as well as other specific terms, conditions and wordings in debt covenants that can preserve value for the company in the event of a range of scenarios, including the acquisition of the company, Pritchard says. “The documents on these deals may run 40 to 50 pages long,” he says. “They can significantly impact a firm's financing flexibility and profitability moving forward.”

Even when lawyers are advising on such deals, he says, they may turn to debt experts to help iron out or renegotiate the details.

On one recent deal, Aequitas assisted Chart Industries with its refinancing of $163.2 million of outstanding 9.125% senior subordinated notes due in 2015. Working as an extension of the company's management team, Aequitas helped assess financing alternatives, leveraged the dynamics between competing banks, and provided input on deal terms and provisions. This resulted in savings for its client in terms of direct costs, such as deal fees and terms, as well as indirect costs, including enhanced process and structural efficiency, Pritchard says.

As a result of these efforts, Chart Industries issued $250 million senior subordinated convertible notes due 2018, pricing “strongly,” Pritchard says, in an extremely volatile market. “The firm realized among the strongest terms and lowest fees for a comparably sized and rated company.”

Despite such outcomes, NYU's Smith says independent advisory firms face critical challenges in the days ahead. “There may be some CFOs who want someone who can whisper in their ear,” he says, in part because investment banks are held in such low esteem these days and an independent firm may be viewed as more trustworthy.

But Smith says CFOs shouldn't underestimate the global reach and knowledge base of the large investment banks and adds that future shifts in investment banking may not favor the boutiques. “Do they know the benefits of an Australian dollar issue versus a euro bond issue? And can an independent firm provide access to the cheapest, global market?” he asks.

Pritchard takes a more upbeat view of his firm's prospects. “There is a great deal of value embedded in the details of these contracts,” he says. “Our view is that the degree to which your entire capital securities process is managed diligently, with calculation and recalculation, the better chance you have that your corporate issuance will produce the results you want.”

For a look at how real estate brokerage company Realogy restructured its outstanding debt amid the financial crisis, see Debt Do-Over at Realogy.