(Jonathan Newton/The Washington Post) GM Mike Rizzo is confident the Nats will be able to “find some hidden gems” late in the draft. (Jonathan Newton/The Washington Post)

For the first time since the Washington Nationals tasked him with guiding their draft efforts four years ago, Roy Clark has never had so many moving parts heading into a draft, the first two rounds of which will be held on Thursday. The Nationals don’t have a first-round pick, the result of signing closer Rafael Soriano under new free agent compensation rules, and don’t select a player until the second round with the 68th overall pick.

Like every team, Nationals scouts fanned out across the country to watch players but with a specific mission in mind. Clark and the Nationals’ scouting department have an idea of the likely top 20 picks, so they have scouted all the players they ranked after that several times. And under rules implemented last year that restrained draft spending, the Nationals will have even less wiggle room with which to pay those picks.

For Clark, there’s no real way to plan for all the dominoes that will fall before them. “We feel good about the process and the guys we’ve gone out to see,” said Clark, the Nationals’ assistant general manager of player personnel. “But you gotta wait and see.”

This winter, the Nationals behaved like a contending team and inked a two-year, $28-million deal with free agent Soriano, who was attached to a compensatory first-round pick. As a result, the Nationals surrendered their first overall pick, which could have been No. 29 overall, to Soriano’s former team, the New York Yankees, who gained the No. 33 overall pick. They also lost the bonus money attached to the selection, perhaps the most inhibitive part of the deal.

Under General Manager Mike Rizzo, the Nationals rebuilt the minor leagues through the draft, luring prospects by paying above the recommended slot money for the picks before new draft bonus pool spending limits were applied last season. Coupled with such a late first pick, the Nationals will be forced to be more creative than ever on how to make their allotted $2.737 million, the smallest in baseball, stretch over their first nine picks. The No. 68 overall pick is the latest the Nationals will have ever picked their first player in a draft since they have been in Washington.

“As scouting director and a scouting department, you don’t want to lose draft picks,” Clark said. “But if Rafael Soriano is our first-round pick in this year’s draft, you know what? We’re going to be okay. That’s the way we gotta look at it. That’s a pretty good first-round pick.”

By losing their first-round pick this year, the Nationals lost $1.758 million in their draft bonus pool – a substantial amount of flexibility which they could have used to perhaps spend on a more talented but expensive player who fell to them. Last year, the Nationals picked 16th overall and were allowed $4.4 million for their first 10 picks.

All 30 major league teams have a cap on signing bonuses for picks in the first 10 rounds, depending on when they pick and the number of compensatory picks they have. The cap ranges from the Houston Astros’ $11.698 million to the Nationals. There are punitive penalties if a team spends more than its cap amount: a 75 percent tax for exceeding the cap by 5 percent, up to a 100 percent tax and the loss of two future first-round picks for exceeding the bonus allotment by more than 15 percent.

Last year, the Nationals exceeded their bonus pool by roughly $100,000 when they signed No. 16 overall pick Lucas Giolito to a $2.925 million signing bonus, enough to incur a fine of roughly $84,000. Clark said the Nationals would be willing, as they have in the past, to do the same if needed this year. “If the right person is there at 68 and we feel real good about, it may cost us a little more and I have a feeling we’ll be creative again in that area,” he said.

Clark said the Nationals, whose starting pitching depth has been thinned of late, would like to add more power arms to the organization through the draft. The Nationals will lean heavily on their scouting department, perhaps more so than before, to discover those pitching arms and other hidden talent scattered across the country.

And it’s possible to find major league talent in the second round or later. Jordan Zimmermann, the best second round pick in Nationals history, went 67th overall in the 2007 draft. All-stars Chase Headley of the San Diego Padres and Giancarlo Stanton of the Miami Marlins were also second round picks, No. 66 in the 2005 draft and No. 76 in the 2007 draft, respectively. Clark, who spent 11 years as the Atlanta Braves’ scouting director before joining the Nationals in 2009, picked six-time all-star catcher Brian McCann with the 64th overall pick in the 2002 draft.

“Our job is to find out where those guys are, where are the hidden gems and take them and have our development staff develop them into big league players,” Rizzo said. “Impact major leaguers are found all over the draft. With our scouting staff, we feel we’re going to turn over all the rocks to try to find some hidden gems and it’ll give us a real impactful draft this year.”

Related: Gems can be found in the second round of the draft