organize project and specify directory for object files in Makefile

If you want to learn make, the GNU make manual is very good, both as a reference and a tutorial. You might want to consider using the patsubst command. The following is a chopped down version of one of my own makefiles that uses it:

OUT = bin/csvfix.exe
CC = g++
IDIR = inc
ODIR = obj
SDIR = src
INC = -Iinc -I../alib/inc
LIBS = ../alib/lib/alib.a -lodbc32 

_OBJS = csved_atable.o \
        csved_case.o \
        csved_cli.o \
        csved_command.o \
        csved_date.o \

OBJS = $(patsubst %,$(ODIR)/%,$(_OBJS))

$(ODIR)/%.o: $(SDIR)/%.cpp 
    $(CC) -c $(INC) -o $@ $< $(CFLAGS) 

$(OUT): $(OBJS)
    $(CC) -o $@ $^ $(CFLAGS) $(LIBS)
    strip $(OUT)

clean:
    rm -f $(ODIR)/*.o $(OUT)

1. Your directory structure seems sensible.

2. I would make an explicit rule for executing the compiler, like

TARGET_DIR=bin
SRC_DIR=src
CXX=g++
CXXFLAGS=
ETC=

OBJS=$(TARGET_DIR)/test.o

all: $(OBJS)

$(TARGET_DIR)/%.o: $(SRC_DIR)/%.cc
        $(CXX) -c -o $@ $(CXXFLAGS) $(ETC) $<

1. You can keep your files in different directories if you like, but that isn't necessary. Add a file or directory to the CVS repository once, and CVS will retain it indefinitely. From then on you can update it, check it in, whatever. If you don't add an object file to the repository, CVS won't touch it. If you want to add a whole directory tree, and you're in the habit of keeping objects there, just make clean before you do it.

2. Make is a wonderful tool, but it has some glaring faults. What you're describing is one of the classic problems: Make is good at using a source there to make something here, but not the other way around. Here are a couple of ways to do what you're trying to do.
   
   

A) Run make in your binary directory:

    ...
    all: myexecutable TAGS

    myexecutable: myobject.o
        $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)

    VPATH = /home/myproject/src
    ...

cd ~/myproject/bin
make -f ../src/makefile

B) Put the objects on the bin directory by brute force:

    $(BIN_DIR)%.o: %.cc
        $(CXX) $(CXXFLAGS) -c -o $@ $^

This will give you a problem with Makefile.depend, which you can approach several ways.

C) Learn some more advanced Make techniques. You probably shouldn't try this yet.