Example:

//Instantiating a Workbook object
Workbook workbook = new Workbook();

Worksheet sheet = workbook.getWorksheets().get(0);

//Get Conditional Formatting
ConditionalFormattingCollection cformattings = sheet.getConditionalFormattings();

//Adds an empty conditional formatting
int index = cformattings.add();

//Get newly added Conditional formatting
FormatConditionCollection fcs = cformattings.get(index);

//Sets the conditional format range.
CellArea ca = new CellArea();

ca.StartRow = 0;

ca.EndRow = 0;

ca.StartColumn = 0;

ca.EndColumn = 0;

fcs.addArea(ca);

ca = new CellArea();

ca.StartRow = 1;

ca.EndRow = 1;

ca.StartColumn = 1;

ca.EndColumn = 1;

fcs.addArea(ca);

//Add condition.
int conditionIndex = fcs.addCondition(FormatConditionType.CELL_VALUE, OperatorType.BETWEEN, "=A2", "100");

//Add condition.
int conditionIndex2 = fcs.addCondition(FormatConditionType.CELL_VALUE, OperatorType.BETWEEN, "50", "100");

//Sets the background color.
FormatCondition fc = fcs.get(conditionIndex);

fc.getStyle().setBackgroundColor(Color.getRed());

//Saving the Excel file
workbook.save("C:\\output.xls");