The CF worksheet is set up to handle uneven cash flows. You enter CF0 for the cash flow at time 0 and then enter C01 (the $ amount) that occurs F01 times. According to the BA II manual, you can enter up to 24 distinct cash flows.
If the cash flows all happen semi-annually, then the interest rate you use to calculated NPV is just nominal/2. Things get interesting if your cash flows are NOT semi-annual: you can still enter the cash flows according to the C0x logic above, but you will have to calculate the equivalent interest rate to use.
Simple example (using the BA II):
Cash flows of 10 and 20 at 6 months and 1 year, respectively; interest rate is 7% compounded semi-annually
2nd CLR Work
C01 10 Enter F01 1 Enter C01 20 Enter F02 1 Enter
I 3.5 Enter CPT NPV 28.33204976