With early onset BPH in a 50+ male, with inability to empty bladder in one shot, is it reccomended to take the meds w/side affects or manage?

Can try. Can try otc things like saw palmetto. At some point it will progress to needing med like Flomax (tamsulosin) or cardura. Maybe even needing a procedure to open passage with microwave or laser. Discuss situation with family physician or urologist.
Meds. If the urine flow rate,as documented by a uroflow test is clearly abnormal and the bladder does not empty as documented by post-void ultrasound then the first option would be medication,provided no nodule is felt on digital rectal exam and the PSA is not suspicious.Good luck.