What I think would be an excellent addition would be the ability to modify read/write a binary digit DIRECTLY without having use HEX.
As Romaap mentioned, you want to use a logical OR. This is like a "reverse bitmask"; when we want to isolate bits for analysis, we clear all the other bits using AND. When you want to set a bit, you use OR to set the bits you want.
http://en.wikipedia.org/wiki/Mask_(computing)#Masking_bits_to_1We usually represent AND with & or && and OR with | or ||, but there are other symbols sometimes.
Let's say you started with 01000, and you wanted to set bit 1 (that is, 01010; bit 0 is the least significant bit). OR with a value that is composed of the bits you want set.
01000 |
00010 =
01010
In fact, if you look at the disassembly near where a "flag" is being set (i.e. set the flag which indicates the player has the dungeon map), you'll see that they're using the instruction ori = OR with Immediate. The Immediate is almost always a power of 2 (1, 2, 4, 8, 16, etc), which in binary always looks like 0001, 0010, 0100, 1000, etc.
If you don't want to use Assembly, you can use a Gecko register instead. See the 0x86 codetype.