All the programs once loaded run automatically except disassembler. 
The programs in the main programs directory load from the Woz monitor. Simply power up your replica 1, press reset and dump the file using the transfer method described in the replica 1 manual.

Programs in the BASIC directory:

Enter BASIC by typing E000R [return]

Then download the program using your terminal program and it will auto start.

Disassembler:

To load: power up replica 1 and press RESET. Dump program through hyper terminal. To use:  change memory locations $44 and $45 to your starting memory location to disassemble. Type "9F0R" ENTER to run the disassembler. At that point 19 lines of code will be displayed. To see the next 19 lines of code, just type "R" ENTER.