[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers]
"[%InstallPath%]\\proga1.exe"="WIN98"
"[%InstallPath%]\\proga2.exe"="RUNASADMIN"
'......

[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers]
"G:\\Program Files (x86)\\Proga\\proga2.exe"="RUNASADMIN"
"G:\\Program Files (x86)\\Proga\\proga1.exe"="WIN98"
'.........

Declare Function RegSetValueEx Lib "advapi32" Alias _
    "RegSetValueExA" (ByVal hKey As Long, ByVal _
    lpValueName As String, ByVal Reserved As Long, _
    ByVal dwType As Long, ByVal szData As String, _
    ByVal cbData As Long) As Long

Private Sub Command1_Click()
    Dim Str As String
    Str = "REG ADD " & Chr( 34 ) & "HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers" & _
        Chr( 34 ) & " /v  " & Chr( 34 ) & "G:\Program Files (x86)\FaxBoom\proga1.exe" & Chr( 34 ) & _
        " /t REG_SZ /d " & Chr( 34 ) & "WIN98" & Chr( 34 ) & " /f"
    Shell Str, vbNormalFocus
End Sub

Private Sub Command1_Click()
    Dim Str As String
    Str = "REG ADD " & Chr( 34 ) & "HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers" & _
        Chr( 34 ) & " /v  " & Chr( 34 ) & "G:\Program Files (x86)\Proga\proga1.exe" & Chr( 34 ) & _
        " /t REG_SZ /d " & Chr( 34 ) & "WIN98" & Chr( 34 ) & " /f /reg:64"
    Shell Str, vbNormalFocus
End Sub

These flags can be specified in the samDesired parameter of the following registry functions:
RegCreateKeyEx 
RegDeleteKeyEx 
RegOpenKeyEx 

'Registry Constants
Public Const HKEY_LOCAL_MACHINE = &H80000002
'...
'Registry Specific Access Rights
'...
Public Const KEY_ALL_ACCESS = &H3F
'новые ключи для доступа к 64-х битному реестру!
Public Const KEY_WOW64_64KEY = &H100
Public Const KEY_WOW64_32KEY = &H200
...

Public Function SetRegValue(hKey As Long, lpszSubKey As String, _
                    ByVal sSetValue As String, _
                    ByVal sValue As String, reg64 As Boolean) As Boolean

    On Error GoTo ErrorRoutineErr:

    Dim phkResult As Long
    Dim lResult As Long
    Dim SA As SECURITY_ATTRIBUTES
    Dim Create As Long

    'Note: This function will create the key or
    'value if it doesn't exist.
    'Open or Create the key
    If reg64 Then
        RegCreateKeyEx hKey, lpszSubKey,  0 , "", _
            REG_OPTION_NON_VOLATILE, _
             KEY_ALL_ACCESS Or KEY_WOW64_64KEY, SA, phkResult, Create
    Else
        RegCreateKeyEx hKey, lpszSubKey,  0 , "", _
            REG_OPTION_NON_VOLATILE, _
            KEY_ALL_ACCESS, SA, phkResult, Create
    End If

    lResult = RegSetValueEx(phkResult, sSetValue,  0 , _
        REG_SZ, sValue, _
        CLng(Len(sValue) +  1 ))

    'Close the key
    RegCloseKey phkResult

    'Return SetRegValue Result
    SetRegValue = (lResult = ERROR_SUCCESS)
    Exit Function

ErrorRoutineErr::
  'MsgBox "ERROR #" & str$(Err) & " : " & Error & Chr(13) _
  '       & "Please exit and try again."
  SetRegValue = False

End Function
'------------------------------------------------------------
Public Function DeleteRegValue(hKey As Long, lpszSubKey As String, sValueName As String, reg64 As Boolean) As Boolean

    On Error GoTo ErrorRoutineErr:
    
    Dim phkResult As Long
    Dim lResult As Long
    Dim SA As SECURITY_ATTRIBUTES
    Dim Create As Long
    'Open or Create the key
    If reg64 Then
        RegCreateKeyEx hKey, lpszSubKey,  0 , "", _
            REG_OPTION_NON_VOLATILE, _
             KEY_ALL_ACCESS Or KEY_WOW64_64KEY, SA, phkResult, Create
    Else
        RegCreateKeyEx hKey, lpszSubKey,  0 , "", _
            REG_OPTION_NON_VOLATILE, _
            KEY_ALL_ACCESS, SA, phkResult, Create
    End If
    lResult = RegDeleteValue(phkResult, sValueName)
    RegCloseKey (phkResult)
    'Return obtained value
    If lResult = ERROR_SUCCESS Then
        DeleteRegValue = True
    Else
        DeleteRegValue = False
    End If
    Exit Function
ErrorRoutineErr::
    DeleteRegValue = False
End Function

'...
        ElseIf (InStr(WinSysVer.VersionName, "Windows Vista") >  0 ) Then
'...
            ElseIf InStr(Command, "/ProgaInstReg") >  0  Then 'установка ключей реестра
                If OStype = "x64" Then
                    SetRegValue HKEY_LOCAL_MACHINE, "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga1.exe", "RUNASADMIN", True
                    SetRegValue HKEY_LOCAL_MACHINE, "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga2.exe", "WIN98", True
'...
                Else
                    SetRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga1.exe", "RUNASADMIN", False
                    SetRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga2.exe", "WIN98", False
                End If
            ElseIf InStr(Command, "/ProgaUninstReg") >  0  Then 'удаление ключей реестра
                If OStype = "x64" Then
                    DeleteRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga1.exe", True
                    DeleteRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga2.exe", True
'...
                Else
                    DeleteRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga1.exe", False
                    DeleteRegValue HKEY_LOCAL_MACHINE, _
                        "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers", _
                        AppPath & "proga2.exe", False
'...
                End If
            End If
        Else
'...