can you not record your song if it's made of separate seq?

i haven't got the extra memory yet but i plan too. i always here people talking about transfering their songs to the comp in one wav file, but can you still do that if one song is split up into 5 sequences? If you would like to go into program mode during playback? Even if you wanted to add effects and control them manually?

You'd normally use Song Mode to chain the sequences in order.
But in Song Mode you don't have access to the Main screen, you're limited to what you set up before entering Song Mode e.g. sliders for the Active Program. (Or external FX, of course.)

so if i want to manually make changes, while on the program or main screen, i should just run the main out to the comp and record with some program?

You can set up the order of patterns in song mode and then convert the song into a pattern; it mentions it in the manual, hopefully this is of some use to you.