After catheter removal, the antifungal of choice would depend on the offending organism and sensitivities.
If fluconazole is deemed to be an appropriate choice, the recommendations is 200 mg on day 1, then 100 to 200 mg once daily for 2 to 4 weeks.  
I am not familar with every other day dosing for treatment, although 200 mg of fluconazole every other day has been shown to be effective in fingal peritonitis prevention when patients are on antibioitcs.