from qgis.PyQt.QtCore import *

def drawLay ( namee, x1, y1 ) :
    lay = QgsVectorLayer('Point?crs=epsg:2039', namee , 'memory')
    pr = lay.dataProvider()
    lay.startEditing()
    fet = QgsFeature()
    fet.setGeometry( QgsGeometry.fromPointXY(QgsPointXY(x1,y1)) )
    pr.addFeatures( [ fet ] )
    lay.commitChanges()
    lay.updateExtents()
    QgsProject.instance().addMapLayer(lay)

# create two layers
drawLay ( 'aa', 150000, 400000)
drawLay ( 'bb', 150100, 400000)

#write this layers into geoPackage
GpName = r'c:tempgpk_file.gpkg'
options = QgsVectorFileWriter.SaveVectorOptions()
options.actionOnExistingFile = QgsVectorFileWriter.CreateOrOverwriteLayer
options.EditionCapability = QgsVectorFileWriter.CanAddNewLayer
for layer in  iface.mapCanvas().layers() :
    namee =layer.name()
    print (namee)
    options.layerName = namee
    _writer = QgsVectorFileWriter.writeAsVectorFormat(layer, GpName, options )

from qgis.PyQt.QtCore import *

def drawLay ( namee, x1, y1 ) :
    lay = QgsVectorLayer('Point?crs=epsg:2039', namee , 'memory')
    pr = lay.dataProvider()
    lay.startEditing()
    fet = QgsFeature()
    fet.setGeometry( QgsGeometry.fromPointXY(QgsPointXY(x1,y1)) )
    pr.addFeatures( [ fet ] )
    lay.commitChanges()
    lay.updateExtents()
    QgsProject.instance().addMapLayer(lay)

# create two layers
drawLay ( 'aa', 150000, 400000)
drawLay ( 'bb', 150100, 400000)

#write this layers into geoPackage
GpName = r'D:tempgpk_file.gpkg'
for layer in  QgsProject.instance().mapLayers().values() :
    options = QgsVectorFileWriter.SaveVectorOptions()
    options.actionOnExistingFile = QgsVectorFileWriter.CreateOrOverwriteLayer #Update mode
    options.EditionCapability = QgsVectorFileWriter.CanAddNewLayer
    options.layerName = layer.name()
    print("Update mode")
    _writer = QgsVectorFileWriter.writeAsVectorFormat(layer, GpName, options)
    if _writer:
            print(layer.name(), _writer)
    if _writer[0] == QgsVectorFileWriter.ErrCreateDataSource :
        print("Create mode")
        options.actionOnExistingFile = QgsVectorFileWriter.CreateOrOverwriteFile #Create mode
        _writer= QgsVectorFileWriter.writeAsVectorFormat(layer, GpName, options)
        if _writer:
                print(layer.name(), _writer)

GpName = r'c:tempgpk_file.gpkg'
firstt = True
options = QgsVectorFileWriter.SaveVectorOptions()
for layer in  QgsProject.instance().mapLayers().values() :
    if firstt :
        firstt = False
    else :
        options.actionOnExistingFile = QgsVectorFileWriter.CreateOrOverwriteLayer
        options.EditionCapability = QgsVectorFileWriter.CanAddNewLayer
    options.layerName = layer.name()
    _writer = QgsVectorFileWriter.writeAsVectorFormat(layer, GpName, options )